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How do I handle inaccessible DOIs when citing papers?
When writing a paper, it's not that seldom, that I want to cite papers where a DOI is given but cannot be accessed (anymore). Quite frequently, the corresponding DOI is also presented within the PDF document of the paper that I want to cite, which is also not accessible (anymore).
The intention of DOIs was to guarantee permanent access to documents and unify it, but in reality, some are broken over time. Furthermore, not every DOI lookup website does have a complete list of all DOIs.
My primary question is: Is there some common practice how to handle this situation? Should I provide the DOI as well in my references, even though it is not accessible anymore? (Maybe it could still be accessible with some other DOI lookup website?)
What is the best DOI lookup tool? Is there something better than https://doi.org?

This is interesting and surprising (and worrying).  Can you say a little more about what kinds of documents you are seeing with frequently broken DOIs?

@BenBolker I have found several documents with inaccessible DOIs over time while writing papers in the past and I supposed that others would also experience this issue. As far as I can remember, most papers with problematic DOIs were from "smaller" and rather "unknown" publishers (at least for me) and most papers were older or at least several years old. Maybe, some "smaller" publishers even vanished over the years, if one speaks of papers, which are e.g. 10, 15, 20 years old? I will provide a current, concrete example in the answer below.

The few cases where I've had problems were with very recently published papers that hadn't yet been registered somewhere ...

This answer is partially derived from other answers and comments for this question:
Answer for question 1
Despite the fact that DOIs should stay operational/accessible, there exist different reasons why they can become inaccessible:

Some publishers might vanish over time. In this case a DOI authority can be contacted to report the broken DOI.

A publisher might have been merged with another publisher. In case such a DOI is broken, the publisher or a DOI authority could be notified. Usually, the new publisher can fix it.

Some papers might be revoked after publication. In this case a DOI authority should be contacted so that the DOI does not link to a URL which e.g. does not exist anymore.

A domain of a publisher might be down temporarily. This case can be tested by loading other Web pages of the same publisher. If several pages are down at the same time, it's advisable to wait for some hours and then again check the state of the domain. Just some patience might solve this issue.

A technical problem with a specific Website of the publisher's domain might exist. E.g. the content could have been moved to a different location/address. This can be tested, by checking other Web pages of the same publisher. If they work properly, it's most likely that a specific Website has some issue which needs to be fixed by the publisher. Thus, the publisher should be informed.

Sometimes, when papers were recently published, the DOI might already exist but the paper is not yet accessible. In case of very fresh papers, just some patience might solve this issue, until the content is uploaded properly.

Some papers may be fake as well or the publisher might provide low quality papers. In case a DOI is inaccessible, it can be useful to check the trustworthiness of a publisher:

Is it a rather unknown publisher?
Does the website look suspicious?
Are there many typos in the papers or on the publisher's Web domain?
Has the publisher published papers only for e.g. 1 or 2 years?
Are there several papers with inaccessible DOIs of this publisher?
Can you find other inconsistencies?
Optional and not recommended in general: Has this paper never been cited by another author or by very few authors (citation count)? This is not a general recommendation, since every fresh paper has to start with a citation count of zero. Furthermore, it is not always perfectly transparent how the citation counts are created by existing systems. Different systems may report different citation counts. Furthermore, the citation count will hardly be completely accurate. If considered, this should only be seen as some small indicator in combination with other criteria.

The more questions can be answered with yes, the more suspicious it is that the publisher might be fraudulent. It may also happen that this publisher is a "low quality" publisher, which provides low quality papers, without an extended peer review process. In any mentioned case, it is recommended to consider finding alternative papers probably also from other publishers, if possible.

The DOI points to the wrong paper. If a DOI points to the wrong paper or content, then a DOI authority should be informed.

Some typo might exist in the DOI. Finally, it is also possible, that there is just some typo in the given DOI.

In case of doubt, one can also simply perform a web search (e.g. Google or Google Scholar, etc.) with a search string containing the title and the authors of a paper to look it up and to check the corresponding DOI. Sometimes there may also exist a different (and operational) DOI for the paper.
Answer for question 2
https://doi.org and https://crossref.org are two excellent domains for DOI lookup.

I'm from Crossref. The DOI should always resolve to some location, even if the content has moved location on the web or has changed publisher. Can you share the example so we can get it reported? It's possible it's not a Crossref DOI of course (there are several other DOI agencies) but I can find out from the DOI. The prefix does often denote a particular publisher but journals change hands frequently as societies negotiate different publishing agreements so that's not necessarily a failsafe way to solve the problem (which I agree should not be your problem!). Happy to help if you share the example(s) :-)

This is really great to hear! I have had issues with inaccessible DOIs with several documents in the past. The most recent one, which brought me to ask this question is the one provided below, but it was only the tip of the iceberg, since I have had several negative experiences in the past, and I am not sure whether it is the "perfect" example now, because the paper is rather new:

DOI: 10.15680/IJIRSET.2019.0806081;
Data Extraction Techniques for Data on different Environment: A Review;
PDF (where the DOI is included as well): http://www.ijirset.com/upload/2019/june/81_Data.pdf;

currently no result in crossref.org when providing the DOI;
currently no result in doi.org when providing the DOI;

Listed in SemanticScholar: https://www.semanticscholar.org/paper/Data-Extraction-Techniques-for-Data-on-different-%3A-Limited-Kamble/c041a077dd623bbabdd9acb11f9ac0ebea320841

@Anderson Looking to http://www.ijirset.com/volume-8-issue-6.html, I picked another "DOI" and found it to be invalid. I wonder whether the DOIs are fake.

@user2768 I have now checked an older volume (http://www.ijirset.com/volume-5-issue-1.html) with crossref.org, which was issued on January 2016. The first entry (10.15680/IJIRSET.2016.0501001) works, some others showed a result but lead to a completely different paper (of the same publisher) and others did not work at all. I don't know what to say.

@TheoreticalMinimum Yes, this is one of these predatory open access journals that charge you for basically a review-less publication. Im not surprised the DOI is far from official. I strongly advise anyone from using these papers as scientific sources. I'd reject a paper if it used these as references for their work. Look at the journals name "International Journal of Innovative Research in Science, Engineering and Technology", come on. "Journal of everything you'd pay me to publish"

It might be helpful to edit this information (that the original asker's DOI may be fake from the beginning, rather than having expired or something) into the answer (or to write it as an answer), so that it's not only present in comments.

I'm also from Crossref. Broken DOI links aren't good and we do try and fix them. If you get the "DOI Not Found" error page -for example when following this link - https://doi.org/10.15680/IJIRSET.2019.0806081 - it means that the DOI hasn't been registered. If you fill in the form then this error is reported to the appropriate Registration Agency. In Crossref's case we notify the publisher of the error and ask them to fix the problem - it usually gets fixed but if the publisher has ceased operations or isn't a Crossref member anymore the link may not be able to be fixed. Where archiving arrangements are in place the DOI can be redirected to archived copies of the content.

Will the database of crossref.org also be updated, when an inaccessible DOI is reported to doi.org? Can it also be reported to crossref.org directly? What if a result gets shown, but the wrong one (example: 10.15680/IJIRSET.2016.0501002 - Numerical Study of the Effect of Vertical Wind Break on the Trough Collector's Drag Force [http://www.ijirset.com/volume-5-issue-1.html])? Then the form will not be shown.

Publishers fix the DOIs by updating their metadata with Crossref so the Crossref database has to be updated by the publisher. For DOIs that point to the wrong content you can email support(at)crossref.org or the publisher directly - http://www.ijirset.com/contact-us.html.

I know this is not a FAQ of Crossref, but I think this question is related: The journal that OP refers to is from that big subset of journals that are predatory, and likely do not follow standard scientific procedures (e.g. it claims it has an IF of 7.4, self-calculated bogus data). Do journals that would traditionally be listed in Beall's list have access to DOIs/are registered with Crossref? i.e. is there any vetting on who can be register DOIs?

@AnderBiguri Note, publications / journal articles are not the only items which may be attributed a doi.  datacite and zenodo for example equally tag programs (e.g., MoleculeViewer), or whole datasets (e.g. this earth sciences excel file) with this identifier.

@Buttonwood yes, but can I add a DOI to a photo of my cat? to a facebook message? Or is there any filter? where is the filter? does a bogus journal that is trying to make money by exploiting bad scientific methods pass that filter, if it exists?

@AnderBiguri Of course you can get a DOI for a photo of your cat, just say it's a "research output" and upload it to Figshare. A DOI is just a convenient globally unique persistent identifier for "stuff", not a mark of academic or scientific merit. Having a DOI says exactly nothing about the usefulness of a given digital object.

@AnderBiguri For doi.org, the FAQ outline their routine and partners to register items.  But I see researchgate, too.  Note researchgate not only accepts power point files, but the hint to figshare.com accepting any fileformat (incl. doi generation.). E.g. this (cite)

@TooTea thanks, that was the question. I meant more related to Crossref DOIs anyway, but yeah.

While not as volatile as URLs, DOIs still can be revoked or otherwise become unavailable.
In your case, consider if there is a chance that the DOI could become available again (there might be technical difficulties with the host) or whether there is another available source (another DOI). Personally, I would include the DOI in the  bibliography and send a message to the author(s) or the provider (this should not be your problem to solve).
All accessible DOIs can be searched with Crossref (search by title, author, DOI and other metadata).

Most of the time, I think the expectation should be that the DOI will become accessible again in due time, so it's only reasonable to provide it. Consider also providing a second link, e.g., to a preprint or a Wayback Machine snapshot.

Sometimes, a trained eye already attributes the start of the doi to a publisher (e.g., 10.1021 to the American Chemical Society, 10.1016 to Elsevier), an information obviously public (list of examples).  I wonder if a doi regularly remains the same if one publisher is merged with an other.

While DOIs are very convenient, it may actually not be a problem if it is broken. Usually, citations include author(s) name(s), journal name, journal issue, year and possibly page reference and article title. With this information alone you should be able to find a referenced article using the traditional method. Therefore, DOIs can be considered a convenience service with not too big of a fallout if they break. Another convenient "service" is to ask a librarian at your institution if you have difficulties finding a referenced source.
Furthermore, keep in mind that a DOI might simply contain a typo and can thus not be resolved correctly. This can of course also happen with traditional referencing, but there it is usually easier to see that the article from "Nautre" is actually published in "Nature".
Lastly, I would like to point out that the internet has other tools to resolve DOIs than the usual websites. For example, I can easily find the article you mentioned in the comments by using a regular internet search engine.

While it may be possible to find a paper without a DOI, letting DOIs break defeats the purpose of having them at all in the first place.


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Is it OK to ask the graduate chair if my background is competitive?
I'm planning to apply for a M.S. in some Universities at the US, and at one of those, I tried 2 times and failed (bad GRE scores). Now I reapplied, and got better results (Q:159, V:154, A:3.5), but not sure if it will put be in better shape than before. One thing I think it can be a differential is the fact I had an exchange program back at that university. Is it ok to send my grades to the graduate chair and ask if my application is competitive enough?

I am currently the Graduate Coordinator of my department (mathematics, UGA), and it is the season for me to get a lot of emails from would-be or might-be graduate students.  Variations on "Will my application be competitive if I apply?" are the most common question I'm getting.
It's okay to ask this question in the sense that it doesn't bother me at all and I will reply with something.  On the other hand, my reply in most cases has been along the lines "Thank you for your interest in our program.  I encourage you to apply."  I don't think it's in anyone's best interests -- mine, my department's, or the questioner's -- for me to try to evaluate the degree of competitiveness of an application based on very incomplete, self-described information.  I can (and do) address the required components of the application.  If based on the information provided it seems like applying to a graduate (usually PhD) program at a top 50 math department may be a mismatch -- e.g. the applicant's undergraduate major is in something other than mathematics (or a closely related field with many mathematics classes taken) -- then I might explore that a bit in the reply.  But the bottom line is that the application process is relative and competitive, so more than likely we can't know how any given applicant will fare until we see all the applications: i.e., until we go through the application process.  (However, if the self-described profile of the applicant sounds very strong, then I may mention that and encourage them more enthusiastically.)
A few final comments:
1) I can see that it is frustrating to apply, perhaps repeatedly, without knowing one's chances.  But in fact the state of applying for a bunch of things without knowing whether one will get them is a quite common one in later academia, so maybe it would be well to wrap your mind around it now.  (It is not a trivial thing to wrap one's mind around.  I was a really excellent high school student.  When I took the PSATs I expected to become a National Merit Scholar, and I did.  I applied to the University of Chicago not just because I expected to get admitted but because I expected to get a merit-based scholarship, and I did.  I had enough of this kind of expected success that when it came to optional academic competitions / scholarships for which the outcome was in real doubt -- and especially when I didn't see success improving my life in any clear way -- I often didn't apply / show up / give my best effort, to the point of occasionally disappointing my mentors.  Looking back at all this, I must say that I find my behavior quite rational.  But it's not the way that "grownup academia" works.) I spend weeks every year writing a big national grant application; thus far, I've applied for the grant five times, gotten it once, not gotten it three times, and the latest time is pending and will be for many months.  For this grant (NSF), I do get feedback every year, which is helpful overall (though sometimes frustrating in its particulars).  On the other hand, I have applied twice for a smaller, privately funded grant (Simons).  When I didn't get it the first time and got no feedback about it, I was pretty taken aback and felt like complaining about it.  But I thought it through: it was clearly to my advantage to suck it up and apply again.  I did, and I got the grant the second time.  That's grownup academic life -- relatively successful grownup academic life, in fact.
2) There is a kernel of advice lurking in point 1) above.  The best time to ask for feedback is soon after someone has carefully evaluated your application.  If you've applied to a program and didn't get in, you have every right to ask why and how you could improve your application.  It sounds like you think that the reason you didn't get in were your GRE scores: is that what you were told?  If so, given that you improved on the thing they told you to improve upon: that sounds good, you should probably reapply.  Finally, if you already spoke to someone at the program, they told you to improve your GRE scores, and now you have, then it makes considerably more sense to me to continue that conversation with the person who told you to improve your scores: given that your GRE scores have improved so-and-so much, do they think you should reapply?  In that situation you have a better chance of being told something substantive, I think.
3) My program is relatively small (we generally enroll no more than 15 students per year).  In quality, the distance from the very top programs and from "less than serious" PhD programs are each rather large.  Once in a while we "steal" a student from a top twenty program, and sometimes for various reasons we take chances on students with inferior backgrounds.  So our admissions process really plays out a bit differently every year.  I could imagine that a program which is significantly larger, better or worse than ours might have less variation.  I suppose I would nevertheless be surprised if such departments were significantly more forthcoming in their reactions to questions like this, but I don't really know.

Thank you very much for your answer! The university is not one of the most desired, but got some fame now it's on College Football. For the first time I applied, was told the problem was only my LoR, but for the second time they said the problem was LoR and GRE.
What bugs me is that back then when I asked what I could improve, I was told their average for GRE was the 95th percentile (which I think is pretty high, since a student is way more than just the GRE scores).

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Research fellowship after undergrad helps with PhD admissions?
Does taking a year off, to work as a junior research fellow or as a research intern, immediately after one's undergrad help with admission to a better MS (research track, not professional) /PhD program?
If it helps, the field in question is computer science, specifically at the intersection of computer vision and machine learning.

I don't see how it could hurt. The degree of added value most likely depends on what your background is prior to the year as a researcher. If you already have a very strong research background as an undergraduate, an extra year of experience will not help as much as if you have very limited research experience.
I suppose it also depends what you get done during that year. It certainly helped a former student of mine, who didn't get into his desired programs straight out of undergraduate. He took a year to work as an RA in my lab, wrote a first-author PNAS paper, and then was admitted into the top program in his field.

Could you please qualify 'very strong research background'? I want to do this because I have mediocre grades and SOME research experience. Neither stellar. However, I want to only do a PhD only from a top 10 program.

Well, "very strong research background" would be along the lines of a first-author publication in a good journal or conference proceedings.  If you've got mediocre grades and no publication record, for example, you probably will need something extra special to be competitive at top-10 programs. The right research internship could potentially provide that something.

Good answer. But I think one have to keep in mind that, taking a year off != a first-author PNAS paper necessarily. There's hard work, and also luck and good supervising involved. I'm in a slightly different field, but PhD student sometimes publish top-conference first-author work only later in their second year. Don't set the expectation too high.

I believe the value of such internships is greater for "marginal" or "borderline" cases, where the overall case for admissions might be weaker than typical because of poor grades or lack of significant research experience. In such cases. having the extra year of experience can help somewhat. I note that, at least for US admission cycles where people apply in the fall semester or trimester for the following fall, such a path may lead to a potential recommendation writer having known the student for only a handful of months—not necessarily enough time to write a full assessment of the applicant's qualities.

+1 You make a good point about the timing of the application cycle. One might even have to wait another year around to really reap the benefits of a research internship year.

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What should I include in my first email to a potential PhD advisor?
I am applying for Ph.D program, and I need to find an advisor to accept me in his group. I want to send to him a perfect email and get his attention to me.
I would like some opinion on this matter.

Do I include my CV and recondition letter in the first email?
Do I mention my GPA?
Do I straight-up ask them if they are accepting students? Or, do I first attempt to establish a relationship?

The field is renewable energy.

Welcome to Academia SE. In the future, please [edit] your question to improve it instead of asking a new question. Also please be aware of this question.

Also, what is a “recondition letter”? Do you mean a recommendation letter by any chance?

This and this question seem to address most of what you are asking. If you have any remaining questions, please [edit] yours to focus on them and to clarify why the aforementioned questions do not help.

First of all, do not write a generic email to 50 faculty members. You need to focus on a few that you think are a good fit. For example, many faculty members won’t take you because they don’t have funding.
Next, try to make a personal connection: read their papers before, see how you could contribute, and tell them.
If you have a connection to them (you took a class/worked with a colleague of theirs, mentioning them will be a massive bonus (in terms of likelihood of receiving a reply).
Good luck!

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What should a student do when they are the victim of a FERPA violation?
A student was subject to a clear  Family Educational Rights and Privacy Act (FERPA) violation by a professor.
Does student have any rights against the professor?
How should they proceed when they are the victim of a FERPA violation?

Welcome to Academia SE. We cannot really help you with a specific situation with vastly incomplete information. I therefore generalised the question, since this is also what was mostly answered. If you wish to ask about a specific situation, please ask a separate question including all relevant information. Before you do, please read this and this FAQ though.

Under FERPA, your complaint is against the university, not against the professor.  Action against the professor, if any, will be taken by the university.

In the US, you have the right to file a FERPA complaint. The instructions are posted on the Government website.  If the Government decides that there was a FERPA violation, there are two possible outcomes:

They agree that the university will bring itself into compliance, or
They do not agree that the university will bring itself into compliance, and therefore, the university will lose their eligibility for federal funding.

The latter of these is an existential threat to the university; therefore, the first one is almost certain to happen. However, the university could discipline the professor as a way to demonstrate that they take being in compliance seriously.
Beyond this, I think the key question for you is what is your goal?

Students do not have the right to sue over FERPA violations, so  a financial or other settlement for the student is highly unlikely.
If you want some specific action (e.g., being allowed to complete your degree without interacting with this professor), you should request this through the usual channels (start with the department chair, then the dean). You could mention that you believe this is a FERPA violation, but I would avoid making threats.
If you're just angry and want "justice," you could also complain to a dean, department chair, or even ombudsman, or could submit the FERPA complaint. It's hard for students to prevail against professors, however, particularly if this is the first complaint.

Please note that that I generalised the question.

Such actions are a violation of ethics and maybe of law in the US. But it is the student that must seek redress. The university should have an office in which to discuss such things and to which a student can make a complaint. Encourage the student to explore such avenues. The individual should think about what would be fair redress. I would probably expect a public apology, though have doubts about whether it could be arranged.
Department heads and Deans can also be informed, but such things should be done in person, not by email.
Other, more public and radical, options exist, but it is probably best to explore the official ones first and to be aware of the potential negative blow-back consequences of making public claims even when it is warranted.
Such behavior doesn't belong in academia, of course.

Please note that that I generalised the question, which may slightly affect your answer.


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How and why do references in academic papers work?
This question applies both to papers people write to attain a degree, as well as academic papers submitted to journals by researchers.
In theory, the way science works is by building your own original research on top of other people's work. The general idea is that if they did their work well, and you did your work well, then  new insights are revealed and human knowledge as a whole is advanced.
But not everyone is honest and not everyone cares for advancing their field. Bad science is a thing and takes many shapes. So people check each others work, and that includes the references to other people's work. After all, if you base your own work on flawed premises, then no matter how correct you make your own part, the conclusions are still going to be nonsense.
But how does this work in practice? When a reviewer gets a paper, how can they check if the references are reliable? There are so many potential obstacles in the way - many authors and papers will be unknown (so now you need to review those articles as well); articles can be taken from obscure, out-of-print books and journals that are nowhere to be found; paywalls that the reviewer would have to pay out of their own pocket; etc.
It seems to me so impractical as to be almost impossible. How is it done in practice?

But how does this work in practice? When a reviewer gets a paper, how can they check if the references are reliable? There are so many potential obstacles in the way - many authors and papers will be unknown (so now you need to review those articles as well); articles can be taken from obscure, out-of-print books and journals that are nowhere to be found; paywalls that the reviewer would have to pay out of their own pocket; etc.
It seems to me so impractical as to be almost impossible. How is it done in practice?

A properly chosen referee should be familiar with some of the cited references, but probably won't be familiar with all of them. If you're not familiar with any of the references, that's a red flag that you either should decline the referee request, or that the manuscript authors have little knowledge of the field. Leaving that case aside, most referees are probably more trusting of already published papers - at least ones published in reputable avenues. This is mostly reasonable, as they passed some kind of review already, hopefully from a knowledgeable and diligent referee. However, you shouldn't rely on that. Even when true, mistakes can be overlooked.
When you need to read another paper to understand a point/claim made in a manuscript you are reviewing there are some "smell tests" worth using (valuable for any paper you read, really):

Does the manuscript represent the cited paper fairly and without misunderstandings?
Do the results of the cited paper seem plausible?
Are they supported by good arguments?
How has the paper been cited (outside the paper you're reviewing)? After all, someone building on certain results is the person most likely to scrutinize them, so you may find additional support, counterevidence, or limitations in the literature. (Sometimes you can also find a better or more understandable exposition of the results.)

Depending on the specifics of the situation and the standards of the field, it may take more or less time to convince yourself that this paper is probably correct. However, fully "re-reviewing" the cited paper is (usually) not required or expected. If it is central for the manuscript you're reviewing then you might have to, but in that case the manuscript likely already retells the main argument, so it might be less additional work than you envision. What is much more common is to ask/suggest that the authors of the manuscript clarify, support, justify, qualify or hedge their statements as required. That is, you don't have to do the authors' work for them - they're supposed to convince you that their results are valid given the starting points. If they can't explain why the sources they build on are correct, well, they should at a minimum state their limits of their understanding clearly.
So ask if the approximations are justified under the current conditions, or if some external factors were accounted for in an experiment. Point out that technique X has some shortcomings that could affect the result, or if the validity of theory Y hasn't been established in the current regime. Doing so not only helps you figuring out if you trust the results, but also improves the paper for a less expert audience.
As for paywalls, you can ask the editor of the journal to provide you with a copy of papers you need for the review. If that doesn't work, or if the reference is an out-of-print book, inter-library loans can help you out. Ultimately, if the source is nowhere to be found (e.g. a unique original manuscript), or if the referee is unqualified to judge some aspect of the work, they should state so in the report.

The above is largely a description of how a referee could check if the references are reliable, and how they ideally should behave. In practice, however, corners will be cut in a number of places. Some people just aren't very meticulous, others don't want to spend too much time on working for free - especially if the manuscript is incremental, or maybe not all that interesting. Some people might see a famous name in the author list and conclude that the results are probably fine. Any reader should be aware that there are flaws in the reviewing process, and not trust papers blindly - especially when building on them.


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My lab achieves better results than another lab on the same problem – should we collaborate?
Recently, in my research lab we were able to achieve a performance of X % for some problem. This X is far better than the performance Y which was achieved by some other research group for the exact problem, very recently (two months ago).
Yes, we can always compare X and Y and publish the paper alone. But, I was thinking that it is better to collaborate with that research group and share with them the results of our approach.

Should my research group collaborate with them?
Is this a proper way of collaboration?
Should they feel that our group is weaker than they are and that this is why we are trying to collaborate (a feeling of insecurity)?

Could I get some suggestions on this?

Why are you looking to collaborate with them? It's not clear from your question what is motivating this idea, and I feel that this knowledge may be needed to produce the best possible answer.

Don't collaborate just for the sake of collaboration. You need to figure out how you see the collaboration yielding results that could not be achieved if the two labs continued on their individual paths. I'm assuming you are the head of your lab. Figure out your goals and how a collaboration with the other group would help you achieve them. Then, meet with the head of the other lab and share your thoughts.

First, it not just to say "Let's us collaborate with them!" That's not how collaborations start in the first place. To get a collaboration started you need several prerequisites: Genuine interest in the same problems (seems to be given here), similar knowledge and similar goals but also complementing expertise, being open for new ideas from the other side, and most important: Genuine interest in a collaboration in the first place.
Based on the above, I would never approach somebody (or some group) with the question "can we collaborate on this" but always start differently. The start may be different in different cases, it can, e.g., be just informal discussion with an individual without any particular goals besides getting to know each other, it could be a meeting of the workgroups with the purpose of exchanging ideas or it could be an invitation of somebody to give a talk. To see if this may lead to a collaboration is the second step…

Should my research group collaborate with them?

I can't answer it, and probably nobody here can. If you think that a collaboration can be beneficial, than go ahead and contact them.

Is this a proper way of collaboration?

I don't see an answer here either, since I do not see any collaboration yet. I can say that working on the same problems may be a basis for a collaboration. What would also be helpful, would be if your groups attack the same problem with different methods so that combining expertise may be helpful.

Should they feel that our group is weaker than they are and that this is why we are trying to collaborate (a feeling of insecurity)?

I don't think that anybody will jump to this conclusion just because you asked for collaboration. I would also not jump to this conclusion based just on results for one single project (but you told that your results are even better than their results…).

A collaboration is useful if:

you work on a very related or the same problem and
you can offer them expertise or tools that they otherwise wouldn't have and they can offer you expertise or tools that you otherwise wouldn't have.

If you can answer yes to both questions, then you should evaluate whether you can build up trust if you do not know them yet.

+1. We can offer them computational techniques and they can probably contribute in the physical phenomena of the problem.


text:
Balancing short-term academic position and pregnancy
A close friend of mine was offered a three year postdoc position after she finished a previous 3 year postdoc fellowship. She is very excited about the new position but at the same time she is very worried since she and her partner are planning to have a first baby. She mentioned that she felt like she would be taking advantage of the professor who offered her a new position, if she would become pregnant soon and would be on maternity leave for several months, while she only just joined the new lab.
I didn't really know how to respond. Should this really be a concern for her? Or how to balance moving between (relatively) short-term positions and starting a family?

Considerations: 1. What are the laws of the country and the uni she is going to? How are pregnancies handled in, e.g., funded research programmes? 2. Does she have good rapport with the prof? If the funding agency supports maternity leave (e.g. by extending the duration of the funding), it may be an option to actually mention this, if the rapport is good. 3. In the countries I know, if she does not reveal it, the prof has no recourse against her - but, of course, it is morally difficult to leave the prof in the dark. 4. Has she planned how to cope with an intense postdoc job and a child?

1: UK, top 10 university on external funding, but I don't know the scheme. 2: I believe she only met him during the interview as she applied to an advertised job. 3: Are you suggesting that she should disclose to the professor that she is considering to have a child? 4: not sure about this, but when in an academic job, is there ever a good time for this?

That's obviously then not enough information. 3. If she knows the prof well, which doesn't seem to be the case, or if there is a legal model to extend the funding, that also may be attractive to the prof (sometimes it caters to their timing); otherwise, if not legally required, she probably should not state it - perhaps she ends up deciding otherwise? 4. not a better time, but there may be better support networks at different phases in your life. And it depends on their character; some people pull it with incredibly light touch. But she needs to reflect on whether that works for her.

If I understood right, she is not pregnant at this time.
If the post-doc is a one-year appointment, I don't see a problem.  Pregnancies generally last approximately 9 months.  It often takes more than one cycle to conceive.  If she wanted to be sure the birth wouldn't interrupt a 12-month appointment, she and her partner could always wait a couple of cycles before starting.
She may start to want to have an afternoon nap at some point; she'll probably want to bring some extra snacks to work; she would be smart to plan in such a way that she doesn't have to spend a lot of time on her feet in the lab in the last trimester.  Some women find their concentration isn't completely what it was pre-pregnancy.  She might want to build some flexibility into her project(s) in case she finds her productivity is a bit less than what she's used to.
Other than that, the only limitation I can think of would be if she works in a field involving radiation.
If the post-doc is a two-year appointment, then she may want to plan her work flow to allow her to ease back into work part-time after the baby comes, while still making progress with her research.
(How to combine work with care of a young baby is whole topic of its own which I won't get into here.)
Note, my answer would be different if she were about to jump into a tenure-track position, with a solid teaching load and having to build a lab program from scratch.  But this position sounds nothing like that.
Whether or when to start a baby is a very personal decision.  I see nothing objective here to stand in her way if she and her partner want to do this now.
(Note that in the U.S., employment discrimination against pregnant women is strictly prohibited.  I can't imagine things would be substantially different in the UK.  If in doubt, however, http://law.stackexchange.com can help.)

Your last paragraph indicates that it may spare the employers a conflict of interest not to mention the pregnancy plans.

@CaptainEmacs - Agreed.  Family matters have no place in any discussions that take place before a contract is signed.  She might want to get the advisor's help in planning the actual work flow at some point, but the nature of the relationship that develops with the advisor will help her decide whether the advisor is someone whose opinion she would like to take into account.

"If the post-doc is a one-year appointment, I don't see a problem." I think you may be underestimating the timing issues involved.  First, the academic in question is planning now to have a child.  An academic position would probably not start for several months, or perhaps not even longer.  (E.g. I know someone who just got offered a postdoc to start in Fall 2017.)  If you're telling someone to wait until the birth would take place after the end of a one-year postdoc, then in particular you're telling them to delay the birth until the end of the job....

....The issue with that is that if the academic does not have the same academic job the next year, then she will want another one, and the situation will be much the same.  In particular, you write "Note, my answer would be different if she were about to jump into a tenure-track position, with a solid teaching load and having to build a lab program from scratch. But this position sounds nothing like that." But that could be exactly what she is doing, or wants to be doing, immediately after giving birth.

@PeteL.Clark - She could also be planning to move to a Third World country to take a three-year child-rearing break, and commune with nature.  Look, if her post-birth plans are relevant to the question, they should be spelled out in the question.  We can't be expected to have a crystal ball, or to imagine all the things that were not stated in the question.

@PeteL.Clark - "I know someone who just got offered a postdoc to start in Fall 2017" - This seems quite unusual  from what I've seen of postdoc hires, but anyway -- if the OP's friend were anticipating a substantial delay, then her main concern would be, is there a nice room where I can pump or nurse.  I really don't understand what your main point is.  I hope you will write an answer, so I can see what you think the constructive advice to the OP's friend should be, because from your comments I am really not getting it.

It's a three year position. i have clarified this in the question.

Please keep the comments polite.

@StrongBad - Could you be more specific?  If I've inadvertently said anything that made you uncomfortable, please spell it out.  Also, flagging can be used when you see a problem with the tone or content of a comment.  Thank you!

@aparente001 nothing specific and nothing over the top. I just wanted to remind you and Pete to be polite.

@StrongBad - Any specific feedback you can provide would be much appreciated, either in the comments or through flagging.  Thanks for keeping an eye on things. Please note that your first comment came to me automatically, even though there was no @, as I was the author of the answer you were commenting on; but the other party may never see your comment without a @ thingie, whatever you call it.

@StrongBad: "I just wanted to remind you and Pete to be polite."  I see no lack of politeness on aparente's part whatsoever.  Reminding people to behave well in the absence of bad behavior on their part can itself be viewed as slightly impolite.  Just a reminder.  (I would recommend deleting all of the last five comments.)

@PeteL.Clark there was a flag that the comments were "rude". I did not feel that any of the comments were so rude as to need to be deleted, but I could see the discussion potentially deteriorating. I did not ping anyone because I wanted the reminder to be general. Lets take this to chat if you want to discuss further.

@StrongBad: I maintain that the claim that aparente's comments are "rude" is utterly baseless.  If you think that they are, you should be able to explain why.  Reminding people to be polite without good reason is impolite.  I suggest the following simple rule of thumb for behavior on this site: do what you would do in your interactions with academic colleagues.  If I were in a faculty meeting and was having a perfectly civil debate with someone and got reminded to be polite by a third party, I would not react well.  You can understand that this is not a positive contribution, right?

Now I'm really not getting it....


text:
Making a short summary before a set of paragraphs?
Of late I noticed that recent books or long articles tend to make a short summary before every set of paragraphs. For example, we might have:
1. Introduction
We so and so ...
Therefore, so and so ....
What is so and so: Let us consider ...
Properties of so and so: We notice that ...
where every boldfaced phrases is followed by a set of paragraphs. For a real example:
http://modular.math.washington.edu/edu/2011/581g/misc/Darmon-Diamond-Taylor-Fermats_Last_Theorem.pdf
My questions are:
1) Is this style of writing really a trend?
2) Is it still a good idea if we are writing an article of moderate length such as a statement of purpose or a short report?
In my opinion, such style seems much more intelligible.

Can you post an example of this style? Maybe link to an article on arXiv?

@Bill Barth: Right, sure. Please see my edit.

Some people might prefer to use LaTeX's \subsubsection instead of \paragraph.  The former has the benefit that it will be numberered, making it easier for a reader to refer to it.

The use of a colon (":") in paragraph headings is non-standard. Stick to a full stop (".").

Ah, it's just LateX's \paragraph{} command.
It's not the most widespread style, but I think it's clearer, too, and I suggest you to go on using it.
What problems could there be? I can only foresee issues with journal articles, if you encounter overzealous copy-editors. A good card to play is "if your house style contains \paragraph{}, I am using it".

It's probably not a trend, but if you like the style, your are free to mimic it. There are millions of scientific articles written every year. Tracking or finding trends in style in these articles is probably not worth it. It almost certainly varies among scientific communities and among what journals and conferences prefer.

Thank you for your prompt reply. Do you have any opinion on question 2)?

Not really. Try it. If you don't like it, remove it.

@Brian: Similarly, if your journal's editor doesn't like it, remove it. :)


text:
Does getting an offer from a U.S. phd program earlier than normal mean getting a relatively better offer?
As I browse the Internet, I observe that a U.S. phd program may send its offers to the applicants at different time points.
However, does this difference imply the difference in favor? I mean, does getting an offer earlier imply getting a better offer?

What country? It makes a difference, although there can be differences even within universities, let alone between nations.

No. It just means they're interested, it has nothing to do with the quality of the offer.

I'll assume you are talking about a department that admits students via a single admissions committee (rather than offers from individual professors or groups, in which case all bets are off regarding the timing).
As a general rule, getting an offer earlier is a sign that the committee is more interested, but that doesn't mean the actual offer will be better in any concrete sense.  Often there will be a first wave of offers, which may be followed by additional offers depending on how many people seem likely to accept.  Sometimes the further offers are explicitly described as a waiting list, but sometimes the only distinguishing factor is that they come later in time.

Probably not. My institution has different sources of phd funding - for instance, from national bodies, overseas collaborations and agreements, internal scholarships in order to promote different initiatives (for instance we might have an agreement to fund 5 scholarships for students from Asia) etc. In addition, research projects might have PhD scholarships attached and these happen all the time. Therefore, we recruit new PhDs throughout the academic year. (and occasionally have new PhDs start outside of the standard start of the academic year)

In general, most graduate departments have "flat" offerings to their incoming graduate students—everybody gets essentially the same level of financial support. There may be some differences based on the students' abilities to secure their own funding (for instance, a "bonus" or "premium" if they bring in an external fellowship).
Now there are some cases where graduate students have special fellowships for outstanding graduate students, but these are often highly competitive and require an additional round of review before the awards are made. However, the one example I am aware of announced the decisions at the same time as the admissions decision itself. So, unless you've been told at the time of admission that something like this might be possible, I would assume that your offer is going to be essentially the same as all other graduate students coming in. The school likely just wants to move quickly to get a better chance at retaining students it thinks are especially qualified.

In my department also, we can sometimes arrange fellowship awards for special candidates, and as I recall, we can inform these candidates around the time of their admission offers.  Unfortunately, these awards are rather small, and this+standard offer is still less than many other departments' standard offers.

In my application process, I have seen or heard about several schools using "small fellowships" as additional incentives for their top students. Usually an additional payment for their first year on the order of $3-5k.


text:
Is it appropriate to reply every time to a professor's "thank you" email?
I want to know, since I am not a native English speaker, whether or not it is appropriate to reply to a thank-you email from a professor?
For example, if every time you get an email from a professor saying "Thanks," you reply "no problem" or "you are welcome."
Could it turn out to be annoying or offending if one replies to every "thank you"?
I realized sometimes misunderstanding may unnecessarily arise because of cultural differences. If one does not reply to a thank-you email from a professor, then would the professor be accordingly offended? On the other hand, if one constantly reply "you are welcome" or something like this, would he be instead considered prudish?

It can't hurt to say "You're welcome."

@BillBarth: Ah, I see. Thank you so much :). Just want to get some feeling about how people in a different culture would feel and think :)

@BillBarth: But could it turn out to be annoying or offending if one replies every thank-you?

How many thank you emails do you get from your professors? Is it really that many?

@Comeseeconquer I think you may have written this ambiguously.  I think you mean "Is it appropriate to send a thank-you email in response to every email from a professor," but I think Bill Barth is reading you differently.

Ah, I did not mean that... I just make a hypothetical situation so that I would have a ruler in mind to handle this. Because I always reply to every thank-you, I am afraid whether this habit would backfire my sincerity.

@BenWebster: Thank you very much for your attention. The truth is Bill Barth read it correctly, my question is what I intend to express. :)

@JeromyAnglim your edit seems to be wrong, per the discussion in comments

@ff524: Thank you very much for your edit! It gets much more close to what I was trying to say.

I'm still a bit confused, but I think I understand. You receive an email from a professor saying "thanks". Should you as a student reply "thanks" to an email from a professor that says "thanks"?

@Jeromy I think it was meant to be Should you as a student reply to an email from a professor that says "thanks"?, not necessarily Should you as a student reply "thanks" to an email from a professor that says "thanks"? (the OP didn't say anything about the content of the reply)

@JeromyAnglim: Totally consistent with what I was trying to say if you say "reply 'no problem' or 'you are welcome' to a series of emails from a Professor saying 'thanks'"!

FWIW, your English in this question is better than that of most native speakers I know.

I'm usually the one thanking my professors... Anyway, in your situation I'd add the "You're welcome" reply in any mail that would need to be sent (if there is any) and if not then let it be. That's what I'd do, but social conventions may change in very local ways.

@LightnessRacesinOrbit: Thank you for your praise. The English is good because ff524 helps a lot! :)

Also note that if a professor signs off her email with “Thanks” (as many do with “Best” or “Cheers”), do not take this alone as an invitation to send a response!

For what it's worth, I'd feel that "no problem" is very slightly less formal than "you are welcome" (or even "not a problem"). For example, I'd expect someone to be a little more likely to respond to a friend or colleague with "no problem", than a professor or person in authority. It could also come down to other factors such as the region (e.g. I hear "no problem" in public places such as eateries around New York more than I do in Texas). But some might even say "you're welcome" comes across slightly arrogant as this answer explains .

@AssortedTrailmix: Thanks so much :) You know what, sometimes all these tacitly understood usages and their connotations truly ... When I want to be polite by saying "you're welcome" then it may turn out to be considered "arrogant". I will take care of these subtleties, much appreciated.

Email exchanges need to end at some point.
If the professor's email is a simple receipt of correspondence, then I don't think there's a need to reply. However, if the professor has initiated a larger email then a reply is probably appropriate. See these examples:
Thanks sent as a form of receipt:

Student: Hi Professor Smith,
  I've run the analyses you have suggested (see attached),
  Cheers,
  Mike

Then the professor replies:

Pofessor Smith: Thanks for that

In this case, I think there is no need for the student to reply "You're welcome".
It wouldn't be a big problem, but it would be mildly distracting for the professor. Email exchanges need to end. The professor's "thank you email" was already a confirmation email indicating receipt of your original message.
Thanks sent by professor as part of a larger email initiated by the professor
Imagine the professor sends you an email that provides detailed information that also includes a thank you.

Professor Smith: Hi Mike, well done on your work in the lab the other day. You did a really good job of fixing that equipment. I really appreciate it.
  Cheers,
  Professor Smith

In that case it might be appropriate for the student to reply: "you're welcome".

Ah that is a great explanation and exemplification.:) I think I am getting some feeling about the etiquette. Much appreciated. It scratches where it itches.

Alternatively, in the final example you could reply "thank you" to acknowledge that you appreciate the positive feedback and being appreciated instead of "you're welcome" which sounds a little like the Professor owes you one.

If the entire content of response is "thank you," there is absolutely no expectation that you will respond to those emails with "you're welcome" or "no problem" or anything else. As I've used them, the point of the "thank you" email is usually just to acknowledge that the email being replied to you has been received and read. There is no need to acknowledge the acknowledgement.
In this sense, an email reply that consists only of "thank you" can be used as an invitation to end an email thread. Saying your "you're welcome" will be read as polite but it might get annoying if it seems like you are always trying to get the last word on every thread. If it's really just "thank you", you can safely skip the reply.

Thank you, a great answer that resolves the issue. :) You catched my question, and, yeah, if nobody ends the conversation first then we have a loop of infinite length... But now I can see what is to be tacitly understood.

I'm not a native speaker either but generally speaking "thanks" does not mean "please waste another 2 minutes of my time".

Thank you for your interest. But did you read the question?

EDIT: Apparently, I'm wrong, and some professors write a lot more "thank you" emails than I do.
I think you mean "Is it appropriate to send a thank-you email in response to every email from a professor," and I'm answering that question.
It probably depends on the professor, but I think it's a reasonable approach toconsistently send a short reply to acknowledge emails from a professor.  It doesn't have to necessarily be a thank you (for example, if setting up a meeting, you can just write "See you there.", but it's always helpful to receive a reply showing you an email was read.

The question you answered has already been asked and answered here; since your answer does not apply to this question, I suggest editing or deleting it.

Thanks so much. I got what you mean. Nevertheless, my question may be viewed as the converse of the question you answered... :) Your answer is still very helpful for me.


text:
If the editor handling my paper is a retired professor, then would it be fine for me to inquire about my paper status?
I have a paper under review at a journal for 2.5 months.
Given: 1) it is a short paper taking only two pages, 2) I know that the editor handling this paper is a retired professor, and 3) I have submitted several short papers (the number of pages is < 5) to this journal and all of them were handled by this editor. Yet according to the past events, 1 month is the longest for a first decision. Then if it is fine for me to send a polite, short email to inquire about my paper status in order to "remind" the editor?

Is 2.5 months unusually long in your field? In some fields this would be much too fast to expect a decision, even for a short paper. And I don't think the editor's retirement status should make any difference either way.

@NateEldredge: Ah, I just naively think that maybe the editor is thus somehow less busy than an editor being a full-time professor at the same time :)

I see no reason to assume that: retired people may be just as busy, but with other things. But it's kind of moot anyway; at this point you are probably waiting on the referee, not the editor.

@NateEldredge, Thanks. Your first comment reminds me of revealing important information: I have submitted several short papers (the number of pages is < 5) to this journal and all of them were handled by this editor. Yet according to the past events, 1 month is the longest for a first decision.

@NateEldredge: So may I know if you suggest I inquire about my paper?

I guess it doesn't seem unreasonable, but be prepared to be told "it's still with the referee".

The time frame to a point where a question can or indeed should be sent varies depending on the typical time for that journal, or of similar journals in your field. To me 2.5 months does not sound too long, a decision after one month sounds very quick if I consider a normal set of reviewers also should make their evaluations in that period.
If you think sufficient (relative to what you perceive as "normal") time has passed you can certainly send a short e-mail asking for information. If you have an excuse for asking, in addition of just wanting to know, your mail is far less likely to be perceived as "pushy". But, regardless, editors will get hit by such mails fairly regularly and despite some of them or the bulk of them being a source of irritation at times, the question is not strange by any means. It is all down to the tone of the mail.
The fact that the editor is retired should not affect any aspect of the review procedure so I do not see any reason to take that fact into consideration. The journal must appreciate the work the editor is doing, otherwise the editor would likely not be there.

I think this answer could be improved my mentioning a few examples of what an "excuse" might look like.


text:
How would it look like from reviewers' point of view if one submits off-topic works for application to phd programs?
By a scientific work I mean any work of mine that either belongs to my field or belongs to some related fields of my field. A work that is not a scientific work is called off-topic.
Since I occasionally (but seriously) compose poems and popular songs, I am wondering whether it is suitable to integrate these off-topic works into the collection of my scientific works that is prepared for application to phd programs.
My principal concern is that I am unsure about how this act would look like from the reviewers' angle? Would it be deemed an affectation? Indeed, my wish is merely to present more of me.
Hope ladies and gentlemen (preferably with experience as a reviewer for phd admission) would share me your thoughts, much appreciated.
If answering this question requires more information, please feel free to state that.

Being a mathematician, I must address a logical loophole: I will assume that your field is a STEM field and thus poetry and songs are actually off-topic (and not just called off-topic).

How many legs does a dog have if you call the tail a leg? Four. Calling a tail a leg doesn't make it a leg.
  -- Abraham Lincoln

Assuming this: no, I would not submit such creative materials as part of an application to a STEM PhD program.  I wouldn't go so far as to say that submitting such things would be deemed an "affectation": however, unless you make a clear connection to your chosen field, they are simply not relevant.  Including irrelevant things is not a disaster, but it does indicate that you don't have a clear understanding of what is relevant information in the consideration of your own prospects in that program, which is not great.
Most such applications have a personal statement.  Mentioning somewhere in the personal statement that you write poetry and songs sounds about right to me: from one human being to another, that is interesting, and personal statements are often not so interesting.  But be careful here: a "personal statement" is not a statement about you as a person!  It is really an essay explaining why you would be a strong candidate for the program, so things which are not relevant to that should not be dwelled upon.
Many programs do look at the personal statement as a writing sample -- and good writing skills are very relevant in any PhD program, probably more so than any other single quality -- so if you are an unusually good writer the personal statement would be a good opportunity to show your superior skills.  However, trying to do that in the genre of either poetry or song would be so risky and open to negative reactions based on personal taste that I wouldn't recommend it: after all, in most STEM programs you need to be able to write prose, not poetry, and you are not really permitted to burst into song.  This is probably a "color between the lines" situation.
Added: I spent four (recent) years on the committee in charge of graduate admissions in the UGA mathematics department, and I still read some PhD applications every year.

Many thanks for your holistic and sincere advice, Prof. Clark.

+1 for "but it does indicate that you don't have a clear understanding of what is relevant information in the consideration of your own prospects in that program, which is not great." I've witnessed some bad situations involving graduate students who didn't understand going in what graduate school was really about, and I always look for red flags that that might be the situation when I read applications.  Off-topic materials are definitely such a red flag.

Admissions people are looking for deep thinkers, hard workers, well-rounded individuals, who can collaborate well and communicate effectively.  You can send them a CV that has a section containing secondary things that you're proud of, but which aren't directly relevant to the studies you propose to do.
My experience going to grad school as a returning student leads me to believe that good graduate programs look at the whole person.

Graduate admissions committees in academic fields are not specifically looking for well-rounded individuals, in my experience (on these committees).  Given two candidates, one of whom seems like a "more interesting person" and the other is more narrowly focused on the subject of interest: well, if that narrow focus results in more knowledge, skills or perhaps even enthusiasm for the subject of interest, the narrower person is going to do better.

Also, given that the top graduate programs in my field admit students based on only on their written application, I am confident that "good graduate programs look at the whole person" is not always true.  If you think it is true in your field, maybe you could provide some further delimiting information.  On the other hand, it would be helpful if you could clarify whether you have any direct information about the admissions processes.  Inferring admissions philosophies from a small sample size (1?) does not seem very convincing.

@Pete L. Clark, one rejection, two schools attended (with the corresponding pool of fellow students), memoirs, novels, short stories (e.g. Perri Klass, simultaneously med student and writer). I guess a lot depends on the philosophy of the dept one applies to. Personally, I think that talents with communicating ideas to a broad audience would be a huge selling point. Anyway, what harm can be done by including a CV, containing a short auxiliary section, as a supporting document to the main application? Btw, the admissions process is also a way for the student to find the right fit school!

Sorry I wasn't clear.  I am interested in what field you are in and your geographic location (e.g. in the US?).

I chose U Wisconsin to apply to for CS because their catalog said they encouraged people who had worked in the field to apply.  They accepted me.  A math department didn't.  I chose mathematical sorts of CS for my areas because that's what I enjoyed.  As a trailing partner I transferred to another school, one notch down, this one was an applied math department.  I ended up working with an advisor in another department on an interdisciplinary project.... out of space, see below

Frankly, I don't think your pushing me for my life story, and my unwillingly giving it to you, helps clarify the issues in this disagreement.  Which in terms of our answers, is a bit of a nondisagreement, since you recommended that the poster mention the poetry and songwriting somewhere in the personal statement and I suggested putting it in a supporting section of the CV.

I am not interested in your "life story".  This is an academic Q&A website.  To determine whether advice is good or on-target, it is helpful -- sometimes necessary -- to know about the experience of the person giving it.  In your answer you make a strong claim about graduate admissions.  Since it does not square with my direct experience, I was interested to know whether you have done graduate admissions in a different department or in a different part of the world from me.  If you have never done graduate admissions, that is relevant to those trying to evaluate your answer.

-1 for making claims about things you apparently have no actual knowledge about.

ACTUAL knowledge?  I have no DIRECT knowledge....  I justified my response honestly, by the way -- "My experience going to grad school as a returning student leads me to believe that good graduate programs look at the whole person."

@aparente001: My experiences, and discussions with many colleagues in different disciplines, leads me to the entirely opposite conclusion: being well-rounded helps not one iota. You are judged for your ability to contribute in the field to which you have applied, and that's pretty much it.

From money.howstuffworks.com/personal-finance/college-planning/admissions/ivy-league-admissions2.htm: 'The standard description of a successful Ivy League applicant is "well-rounded," an individual who has proven excellence and unusual achievement across a range of academic subjects and extracurricular pursuits. The Harvard dean says that a well-rounded application shows dedication and is an excellent predictor of future success. That said, the Harvard Web site acknowledges that some successful applicants are also "well-lopsided," showing remarkable talent in a single, focused discipline.'

Granted, that quote is for undergraduate admissions... but I still think that as long as the applicant doesn't appear unfocused, it is still nice to see a creative side.


text:
Should I still use "Dear Prof." to begin an email to a professor that I know?
Let Smith be the last name of a U.S.-grown-up professor you not only have taken part in whose class but also ended up becoming a friend of whom in a general sense; I wonder if it still sounds good if in an email to him one uses "Dear Prof. Smith" to address him. I am not really sure, given this condition, if using "Dear Prof." to begin an email to him would somehow become a tone that he does not like? But, on the other hand, I am afraid using, say "Hi Prof. Smith", would sound like one is exalting himself to the place at which Smith stands as a professional scholar.
The title of this question may not be precise (I am not an English native speaker); please feel free to edit it.

@user4050: Thank you. I have tried to narrow down the scope; does the question now contain sufficient information? Please let me know if it still lacks something. :)

I wouldn't use a job title during personal communications.  "Hi Dr. John" works perfectly well, it shows respect for his accomplishments while being friendly.  Basic rule: Use the same greeting you would if you unexpectedly met them in person.  For some people, that might even be first name.

"Let John be the last name..." While John is a surname, it is much more common as a given ("first") name, to the extent that this choice is slightly confusing.  (c.f. @Tom Church's answer...if I am not myself confused.)  Could we perhaps substitute "Smith" instead?  Or "Chang"?

In a letter you have to make a decision and commit to it.  In an email, you can straddle the fence, and just cop out by writing "Good afternoon."  If you are really and truly stuck between perhaps not being formal enough (thus appearing presumptuous), vs. hurting the person's feelings by sounding too formal (coming across stiff and unfriendly), then you can ask.  For example, "What do you like your students to call you in the greeting of a email or email?  How shall I sign when I'm writing you an email?"

I strongly recommend "Yo Teach!"

In the US, it is very unusual to combine the title "Professor" with a first name. I have never been referred to as "Professor Tom" in my whole career.
You can either write "Dear Prof. Smith", using the family name, or "Dear John". You should only write "Dear John" if you would call him "John" when you speak in person. (For people you haven't met in person, the decision is a bit different; but for people who you know personally, this is a good rule.) For example, my students generally call me "Prof. Church", but sometimes after they graduate I invite them to call me Tom; in this case, it would be perfectly appropriate to send me a letter beginning "Dear Tom".
I would use "Hi John" only to convey a very informal tone. Even with colleagues or students with whom I'm good friends outside of work, I still use "Dear Mary" when contacting them about professional business. For this reason, I don't recommend using "Hi Prof. Smith"; it mixes an informal term with a formal term.

+1; question: No one ever contacts you as "Dear Dr. Church" in this context?

Students sometimes use "Dr. Church", especially first-year students. I encourage them to use "Prof. Church", partly because I prefer it but mostly because many faculty strongly prefer it. My experience in academia (limited to research-intensive universities in the US) is that the only people who are ever called "Dr. Smith" are those who are not in academic positions (e.g. an NSF program director). In other words, in my experience the title "Prof." always takes precedence over "Dr." when both are present.  I fear this discussion inevitably devolves into a collection of anecdotes, though.

While I agree that it is best to use "Prof" in emails to faculty with whom you are not on a 1st name basis, your claim that the only people who go by "Dr. LastName" are in non-academic positions does not accord with my experience.  I know lots of faculty who go by "Dr. LastName" (e.g. yesterday one of my colleagues told me that he encouraged students to call him "Dr. V" since his last name is hard to pronounce).  And while I've heard lots of faculty (esp. women) complain about being addressed by students using their first name, I've never heard anyone complain about "Dr. LastName".

I disagree that "Hi John" is very informal, at least to the ear of a US-born English speaker. I had many professors as an undergrad that wished to exclusively be called by their first names, and I never use titles for faculty now that I am a grad student. It just isn't part of the culture, at least at the two institutions.

If you have already interacted with the professor extensively and also in an informal way, I would just address him by first name. "Dear John" or "Hello John", the first one being somewhat more formal. When you greet him you would say "hello John" I think, and not "Good morning professor John".

Let Smith be the last name of a U.S.-grown-up professor you not only have taken part in whose class but also ended up becoming a friend of whom in a general sense

Given that, I imagine you've emailed Professor Smith before? If they sign their emails, check how they do so. That is usually a great hint as to how people wish to be addressed. I have never had a problem with addressing first emails as "Dear Professor XYZ" and then shifting towards a more informal "Hi [however they sign their emails]".
In addition, I would add that "Dear" can come off as either dated or overly formal. Although it wouldn't hurt necessarily, it might come off as trying a bit too hard if you open every email within a single conversation this way. However, the older the professor is, the more they tend to appreciate such gestures (at least in the US).
As long as you're using conventional salutations and parts of their actual titles and names ("Hi John" is often ok, "Yo Johnny-boy" is definitely not ok)  you should be fine. If they correct you, respect the correction but do not worry that a bridge has been burnt. The US just doesn't place relationship-ending weight on titles and email formalities. That said, if you're very worried, it never hurts to ask.

"Dear"?  Is he dear to you?  "Hi" is no good either, and is reserved for friends.
No, the answer to this is to just address him/her directly:  "Professor Smith,".

This answer is inconsistent with all style guides I have ever seen for professional communication in English. (Conventions in other languages may be different.)

@TomChurch: You didn't address the "Dear" part, though.

"Dear X" is an idiom in professional English.  It does not denote that the recipient is actually dear to the writer.  See also "Sehr geehrter Doktor Schmidt" and "Je vous prie de croire, Monsieur, à l'assurance de mes salutations distinguées".

For what it's worth, possibly someone should note very specifically that this answer, plausible in some world, is in fact possibly-unfortunately inaccurate in the U.S. and western Europe, in all my experience. That is, idealized interpretations of cliches are not useful, etc.

Thank you. The word "dear" is also equivalent to "highly esteemed or regarded", as you may check any dictionary; so yes, such a professor is dear to me.


text:
Suggestions for an alternative grading system
I'm designing a leadership development program for a graduate college at a research university. As part of the project, I've designed a summary sheet which each participant will receive. The summary is designed to give them an impression of their overall leadership development. It includes an "overall leadership score," which is currently shown as a number on a 1-10 scale.
My intent is for all students to begin the program at a baseline level of 5. Students who demonstrate multiple positive leadership traits will raise their score above a 5. Students who show a lack of these traits will lower that score.
However, I'd like to replace the 1-10 scale since it will be difficult to keep the baseline or average score of 5 from being equated with a 50, an F, etc. For the same reason, I've avoided the use of a letter scale.
Does anyone have suggestions on an alternative grading system that is well suited to this type of grading task? I'm also trying to find something that won't be too discouraging for students whose leadership scores are below average (seeing a 0 or an F would not get the right message across).

Do you really expect your students not to convert whatever grading system you adopt into a standard A-B-C-F scale?

I would suggest a rubric that includes the desired qualities of each category.  If you're really worried about the scale, don't include the numbers or letters at all, or change to something like Roman Numerals.  I would not include more than four or five categories, unless you can really break down differences. E.g.,

I. Not making progress. The student needs to improve his/her leadership skills, to include participating in mentor/mentee relationships with junior students, or actively seeking out lead roles in the lab.
II. Pre-leadership.  The student is new to the lab, and has not yet developed leadership roles.  The student should start looking for opportunities for leadership, and should begin considering the type of leader he or she wants to be.  The student should thoughtfully observe other leaders and their leadership styles.
III. Making progress.  The student is actively engaged in a leadership role in the lab and/or has made mentor/mentee relationships with junior students.  The student should continue to develop his/her leadership skills in these roles.
IV. Excellent leadership development.  The student has actively developed his/her leadership opportunities, and is capable of independent leadership in the lab.  Other students view him/her as a quality leader and are comfortable going to the student for guidance.
V. Phenomenal leader.  The student is qualified to independently lead large groups of other students, and is able to mentor others in leadership roles.

In this example, I would start everyone off at (II).  Everyone will know they should look for leadership opportunities, and it should be relatively easy to get into the (III) category.   Obviously, this is only an example, and can be tailored to your situation.

I'm also trying to find something that won't be too discouraging for students whose leadership scores are below average (seeing a 0 or an F would not get the right message across).

I do think having some sort of forcing function is necessary; otherwise, what is the reason to improve?  In my example, you could tone down "Not making progress" (or take it out), but if you do want to show students who aren't improving that they need to, you should have at least one negative category.

It is not clear what you are trying to accomplish with your grading system. If the point is to evaluate/rank the students then 1-10 is probably as good as anything else. If it is to be used as a formative tool then using an absolute scale is probably less helpful and what the students need to know are their relative strength and weaknesses and areas that they can improve on. What this means is that a student who gets a 9 out of 10 still can improve his/her leadership, similarly a student with a 2 out of 10 likely has leadership areas/traits that can be improved more than others. It is not clear to me that the competition aspect of ranking the students will be beneficial in this case. If you go with a relative scale you could just make the total of the numbers sum to 10 (or 1 or 100). Better would probably be a stacked bar or pie chart so it is clearer that comparisons across individuals are meaningless.
I think the best "grading" system for leadership is probably one that doesn't assign presence/absence of leadership traits, but rather one that characterizes in positive terms the type of leadership each individual is most suited for (e.g. the managerial grid model).

It's a challenging question. I believe your goal is to measure progress and not overall leadership-levels. That is, Student A could enter with strong leadership skills and would start at a 5. Student B could enter with weak leadership skills and would also start at a 5. If Student B shows more progress in improving their leadership skills, then Student B should end up with a 7 (for example) while Student A who was a bit lax and did not improve might end up with a 4 or even 3. The goal, as I understand, is to measure improvement only.
If my understanding is correct you have a challenge in that if students know this, they will try to corrupt (by under-performing) the baseline. Then they will naturally appear to have improved more than they really have giving them a better grade not by improving but by gaming your grading system.
You could structure it by learning outcomes whereby points of improvement are each an outcome. For example:

Outcome 1: Improve ability to communicate to those in subordinate positions
Outcome 2: Improve......

By this, you do not fix the levels but show what areas in which each student should actually improve. This also makes it extremely clear what the goals are. You could assign a certain number of points per outcome (10 for outcome 1, 5 for outcome 2, etc.) to sum up to a total score as well.
I know this is not a discussion board but I'd love to hear what you ended up doing.


text:
Is it okay to submit my paper if my code can't be organized now?
Currently, I am working on a model that includes deep neural networks. I am not an expert in coding nor are my colleagues.
I had a hypothesis and it seems to be working. So, I may need to write a research paper and publish it. It takes much time to go through every step and understand in detail the code modules I am using. I somehow managed to join the patches without knowing the coding-related details of each patch. I am taking the patches from the existing GitHub models.
Whenever I see the codes of research papers, they are well-organized by a team of experts. But I am alone and have no team. The research is a part of my thesis. I have no clue about organizing the code.
I have two options:

not sharing the code with the journal
In this case, if the journal asks for the code, then there is no other choice for me and I need to select the second option.

posting the managed code on GitHub and then keeping the link in the research paper.
I am afraid that the readability and the organization of the code impact the decision of reviewers.

Which option should I select now?

If you test your model with code that you don't understand, then how do you know what you're running? How do you know code is using your model?

"Whenever I see the codes of research papers, they are well-organized by a team of experts." I wish!!!

Is it safe to use an algorithm that "seems" to work?

You say "I am alone and have no team" but you also refer to "my colleagues" and you say this is for your thesis, for which you should have at least an advisor if not a group.

FWIW, the code repository can be updated at any point. Though it might be good to include a commit hash or git tag that indicates the version of the original repository at time of publishing/review/etc.

"managed to join the patches" - what "patches" do you mean here?

Recent PhD grad in the computational sciences here. To be clear, it was the general expectation for our program — and I imagine all other computational programs — that if you do not know how to program you learn in the first quarter. Seriously. Have you ever heard of a math PhD who doesn’t know math? Or a literature major who doesn’t know how to read? It is a foundational skill to any computational discipline and, while you don’t need to very talented, you do need to know how to write, structure, and organize your programs. Without those skills, your ability to succeed will be very limited.

@Greenstick They didn't mention what field they're in.  Perhaps this is a PhD student in a natural science field such as biology, and not computer science.

@nasch If you spend some time look at his other questions, his field is ML/DL.

@nasch I read their other post noted in the answer by cag51 where, as edelweiss affirms, the OP states they're in the ML field, which is heavily computational.

Refusing to share code and expecting people to care about your results is like opening a restaurant while refusing to serve any food. Trust me bro, I can cook very well. Huh?

I am not an expert in coding nor are my colleagues.

This is not the first time you have made strange statements about "coding." It is true that you do not need to be an "expert in coding"; you are a researcher, not a software engineer. But understanding and organizing your codebase is something that everyone who works with code needs to do, not just the experts.

I somehow managed to join the patches without knowing the coding-related details of each patch. I am taking the patches from the existing GitHub models.

I would be terrified to publish with code I don't understand. How do you know there are no bugs? I assume you have done some "sanity checks" and things made sense....but still, having to retract a paper because the way you "somehow managed to join" them turned out to be wrong would be unfortunate.

Which option I can select now?

Poorly-written code may count against you, but refusing to share the code will probably hurt just as much. Which option you choose probably comes down to personal preference. To the extent there is a global norm, it is that sharing code is an intrinsically good thing and should be done unless there is a good reason not to (and "I did a bad job" is not a good reason).

To add to this - if you don't understand the code, do you understand the licensing of that code? You can't just relicense other people's code on a whim. If you need to relicense code that isn't originallly yours to meet with the conditions of one of the "patches" (e.g. if you have some code that came from a GPL'ed repo, your new repo must all be GPL) you might find that breaches the license of some of the other patches.

@n00dle - Also, how does OP know that the code he's cobbled together from random bits on GiHub isn't silently reorganising his utterly meaningless results into something that looks meaningful

Most likely NO

It takes much time to go through every step

This left me stunned: didn't you write the code yourself?

I am afraid that the readability and the organization of the code impact the decision of reviewers.

This is likely a correct judgement: If the code is very unstructured, it should not be published because no one — not even you — can claim to understand it.
There are two possible answers.
Understand what happens inside the modules
If by patches you mean invoked modules or libraries, usually reading the docs will be enough to "believe" that they do what they claim to do. No need to understand all of the source code for each module in detail.
If you i) don't understand the docs for the modules or ii) there are no/missing docs for the modules and you aren’t able to understand their source code, then proceed to this third option:
(3): Learn how to code or start collaborating with someone who does
Even people who know how to code can introduce bugs. Low coding quality and logical errors are a serious issue in published research code where even experienced programmers may write software with errors.
Imagine your question the other way around: "I don't really understand math, but I think I've proven something."
No, you didn't.

If you do not understand your code, how do you know that it is actually working, and there is no bug in your code? And how can you publish something you don't understand?
It could be possible that you use synthetic/real data that somehow made the program produce the result you wanted to see. It happened to me before when I tried to modify my correct solution by adding "random" blocks of code in my program to see what might happen.
It was definitely an incorrect solution, yet it somehow produced the correct results for some situations. However, as I  tried to spend more time analyzing other settings, the "random" algorithm completely failed to work.
Looking at the results is never enough to know if the program truly works. You have to spend time analyzing your algorithm. There is no other option. Divide your code into blocks, so it will be easier to know what is going on. At least, you need a good theoretical reason to explain why your program works (and under which situations it may fail).

It's pretty much always the case (in situations that aren't security-sensitive, anyway) that making your code available to the public is the best thing to do.
As others have pointed out, you need to get help organising your code. Not only that, but if you're not clear on how your code works you need to do a code review with someone so that you can figure out if it really is doing what you think it's doing. That will likely include organising your code better: as a professional software developer, my first response when trying to understand badly organised code is usually to try to organise it better. (Obviously having some automated tests will help here, but regardless, "rework it so it makes more sense and then see if it still does what it's supposed to do" will both give you insight and possibly even fix problems in the code.)
If your code is freely available on GitHub you can point people at it and ask for help and suggestions. You may not get any response to requests for help, but if you keep it a secret it's certain that nobody can help you.
Also, depending on your paper, it's possible that the reviewers may need to see the code in order to review it properly. If they did need to see the code and couldn't, and let the paper go through anyway, both you and they may be doing a disservice to the entire academic community by keeping the paper from being properly reviewed.
Next time you do this, by the way, make the code publically available from the start and seek help and advice from others early on, while the code is still a small mess. That will help keep the code from growing into a huge mess.

Beyond what everyone else has already said, it is often useful to use domain-specific knowledge to come up with big-picture checks that, if passed, will give high confidence that large portions of the code are working correctly. This is where you, as an academic, can add value beyond standard software engineering testing practices.
For example, here are some big picture checks from my field (computational science):

In finite elements, you can refine the mesh, plot the error vs mesh size, and verify that the observed convergence rate matches the theoretical convergence rate.

In Newton's method, you can verify that the observed convergence rate is quadratic.

In gradient, or higher derivative, computation, you can compare the computed derivative to a sequence of finite difference derivative approximations for smaller and smaller step sizes, and verify that the two converge to each other at the expected rate.

In the computation of an adjoint code, you can compare (A(x),y) to (x,adjoint_A(y)) and make sure they are the same to roughly machine precision.

These kind of big picture checks are extremely valuable, because bugs (wherever those bugs are) will almost always cause the check to fail.

There is a pretty big difference between trusting well established libraries like PyTorch and grabbing random repos off of GitHub. Especially if trying to combine multiple such repos and hoping that the interfaces work the way you expect.

@cag51 Right. So that would be a "big picture" piece of evidence that is sociological in nature rather than technical. The library is well-established, developed by experts, used by many people for many years. This would generally be a more convincing argument of correctness to a peer reviewer than a battery of unit tests that check it's functions.

There are situations where finding a solution is hard, but verifying the solution is easy. There are other cases where verifying a solution is as hard as finding one, and the only way to verify it is to try finding the solution with a different implementation, check that you get the same results, and pray that both algorithms don’t make the same mistakes.
If you can verify the results of your code, that makes problems with it much less important.

On the whole, yes it's okay. If the code works, it works. Data is data even if the method of collection confusing.
Obviously it's better if you could organize it better. It will also make it more likely that people will use your code and build on your research, which means more citations of your paper. But since you assert it is impossible to organize it, that ship has sailed.
Messy code is better than no code. The critical difference is that a paper with messy code can easily be reproduced. A paper with no code is a different matter.

He/she is far from knowing if the code works.

Code is by definition not data in the computational sense, it operates on data and can also be generative. If we were speaking about a meta analysis of code, then yes, properties of code could be data. But it’s clear that that’s not the case in this instance.

Thank you for this answer, this is exactly the problematic attitude towards code that lead to this kind of scenarios and shows a complete lack of understanding of code. Software isn't a magic box that does things right. It does exactly what you tell it to do. If you tell it something wrong, it does it wrong.
It's like saying "well, we don't know where the data is from or who produced it and any labels are missing, but let's just use it".