I emailed the professor a research idea, he responded: "Just go ahead". Is this an ok?

So, short answer, that's a yes. However, I think that he wants you to start exploring those ideas and get back to him with more content beyond of what you extract from those papers. Some proof-of-concept or similar.


Having decided to become a researcher after long career in industry, should I work independently or start a PhD?

A PhD is training for research.  There's a whole lot of things that happen along the way, but the point of the process is that you gain skills in conducting research.  In addition, you gain the 'worldview of a researcher': how to think critically, assimilate information, analyse data, collaborate and come up with new ideas.

It is, of course, possible to do all these things without doing a PhD.  But the advantage of the PhD is it gives you opportunities that you might not otherwise have: access to resources, specific programmes (eg internships or field studies), people to collaborate with, exposure to new ideas.  Those opportunities can be open to PhD students in a way that they aren't to random members of the public.

A big part of research is interacting with other people, not just working on your own single path.  PhDs force much more interaction than you might do on your own (though it varies by subject).

The other side of 'training for research' is that, once you've come out of the process, you have simple proof that you have been trained.  That's what the letters 'PhD' are code for.  While the experience can be very different at different institutions, a PhD means the holder has untaken a major research effort and it has been validated by their peers, and learned some of the skills of research along the way.

That's the reason that many academic jobs expect you to have a PhD: they don't have time for a free-form assessment of your research skills - the PhD is proof that somebody else has already done that assessment.

By doing research without a PhD, you force people you interact with to do more work to assess your skills.  You can do that by building up a good body of peer reviewed research, which itself is unlikely to care whether you have a PhD (especially if the review is blind).  But in superficial contexts (eg screening for a job, a grant application or an invitation to some event) you're likely to find yourself at a disadvantage.

One advantage with working inside academia is you have more collaborators, but also as you become more senior you can build a research team: when students work for you, you (collectively) can achieve more.  That's difficult to do when you're working independently.

Finally, we can all come up with examples of brilliant people who started working on their subject without a PhD.  I suspect that's much less common than it was in the twentieth century, for two reasons:

Supply and demand: there were many fewer researchers, and the process was much more informal.  Now every tenure job gets hundreds of applicants. Why would you pick one missing critical training?
War and social upset: when you have to work on radar/antibiotics/aeronautics/nuclear physics/intelligence/cryptography at short notice for the war effort, all employment norms go out the window.  When those people came back to civilian life, they already had skills they could use in research.  Or, alternatively, they proved their worth in opportunities available because everyone who would normally take them was away fighting.

(Side note: I come from the UK where PhDs are 3 years on paper and often more like 4 in practice.  The North American process seems like a much more drawn out affair, and the time tradeoffs may be different)


PhD supervisor wants me to quit after break

If your advisor is suggesting that you quit, it is likely that you will have a hard time carrying on with the same advisor.

You maybe need to have a discussion with them about why your performance was bad, and why you needed a break. As it currently stands, it sounds like you had one year in the program without any progress, and then another year where you took a break and also made no progress, so it is two years since you were admitted to the program and you are essentially a new student. From your advisor's point of view, suggesting you quit is good advice as they feel it is unlikely that you will finish your degree. If you want to work with them, you need to convince them that this is not the case.

If you want to continue to pursue a PhD, and you are unable to reach a point in discussion where your advisor is empathetic to your situation and enthusiastic about working with you (not just grudgingly willing to work with you), you probably should either 1: change advisor at the same university, 2: leave your current program and apply to other programs.


Re-analyzed my dissertation work, how should I explain this in a cover letter to a journal editor?

Your submission to the journal will be a separate paper to your dissertation, so it is not a problem if you revise the method and get slightly different results.  Just undertake the analysis with your new method, and write that analysis up in its own right in the new paper --- the journal referee will assess this work on its own merits.  Normally in this case you would cite your dissertation as a precursor to the work in your present paper, but note that your analysis differs from the analysis in that work.  (Perhaps explain this briefly in a footnote.)


Is it ethical to submit a paper with the name of a co-author who cannot be contacted?

This is actually the subject of a blog post over at Adventures in Ethics and Science. In general, it seems that several possible actions are defensible. However, whatever action you take, you should make sure to

Document your efforts to reach your co-author
Let the journal editor know at submission time what's going on

RetractionWatch is full of stories papers that were retracted for having been submitted without a co-author's knowledge. These steps can help you avoid that fate.

Given you've done 1 and 2, your choices are then:

Include the co-author, despite the radio silence, or
Acknowledge the co-author

The problem with the first choice is that authorship signals endorsement of the paper's contents. If the missing co-author has not read and endorsed the final contents, having his name as an author is misleading. However, you can resolve this to some degree by including an explicit statement (e.g., in a footnote) that Author X could not be reached to review the final version of the paper.

The applicability of this choice also depends very much on the journal’s official policy and what responsibilities each of the persons listed as authors have met. I'm sure we can all agree that it would be out of bounds to forge the missing co-author's signature on a form that needs to be submitted with the manuscript! However, even if you have to sign a form stating that all the authors have reviewed the manuscript, you shouldn't do that either - tell the editor you can't, and explain why.

The problem with the second choice (acknowledgement instead of authorship) is that the missing co-author has presumably done enough to warrant authorship of the paper. However, you could argue that an essential part of authorship is to see the paper through to publication - and that if the missing co-author has not done that, he does not deserve authorship. Again, if you do this, you must clearly document the author's contribution in the acknowledgements and alert the editor.

Which action you choose will probably depend on authorship standards in your field and the outcome of your conversation with the editor. Whatever the result, make sure you clearly and honestly communicate the contributions (and lack thereof) of the missing co-author to both your readers and the editor.


No.  I think giving the arxiv link is fine.  One alternative is to have two bibitem entries, one for the journal version and another for the arxiv version.  I find it valuable to include the journal reference, because that shows that the article has been refereed (so its claims gain legitimacy).  But I also see the value of including the arxiv version, particularly if the journal is hard to access.


first round submission VS second round submission in academic conferences

Not knowing the actual system used, nor their history, I can only assume that if you submitted in the first round then nothing in the second round description applies to you at all. Your final paper would be due by 10 September.

It seems as if the conference, in having two rounds, is protecting itself against not having sufficient accepted papers in one round and so permits authors to send papers late for possible review.

If I'm correct, and it seems likely, they want the final paper before they need to make decisions about the second round on 15 September.

If they had wanted you to "resubmit in the second round" they would, I hope, be explicit about that and wouldn't have talked about your paper being "accepted".

You can ask the program committee for clarification, of course. But earlier is better in any case.


Do all preprint servers have the non-updating issue in google scholar

I've been following the Google Scholar Preprint Bug for several years. Claus Wilke (who first characterized the bug in 2014) and I tried reporting it many times. Finally, we caught up with the creator of Google Scholar, Anurag Acharya, in the comment section of Scholarly Kitchen. I was a jerk, which didn't help, but Anurag's responses kept us feeling frustrated.

Anyways, Anurag did shed some light on the cause of the bug in this comment:

  Most preprints/ahead-of-print versions are indexed in early-version model — as they should be. Articles that are indexed in early-version mode are recrawled and reindexed frequently. Changes to their location, their content, their format, their versions are expected to be frequent; this allows changes to be picked up soon.

  Occasionally, a preprint that has been in that state for a while can get indexed in the archival mode. When that happens, updates to that article (location, content, format, versions etc) take longer. Articles that are indexed in an archival mode are reindexed less frequently – as they must, if the indexing system is to use the limited crawl capacity at the journal sites effectively.

Therefore, the bug occurs when a record (preprint in our case) is stagnant for too long. Then that record is placed in archival mode, which triggers the bug, by causing newly crawled versions of the record to be silently ignored. Therefore, according to Anurag's description, the bug is not limited to any single preprint server.

In line with the description, it appears longer publication delays increase the chance of the bug. Perhaps a workaround is to frequently update the preprint so the record never enters archival mode.


How precisely should I implement algorithms from other papers?

It is usually sufficient to say that you tried to optimize both your algorithm and the baseline(s) as much as you could (provided you actually did so).

Before writing your own implementations though, you should first check that the authors of the baseline(s) haven't published their source code. You may even write to them. I've heard all kinds of replies to such requests: from people sending me the code within minutes, to people telling me their code was lost in an old laptop long ago (the paper was 2 years old...). If they don't have the code, you can ask them how they would/did implement their algorithm.

It would be good practice and very beneficial for the community if you then publish both the code for your algorithm AND (if you implemented them) the code for the baselines.


Statement of Purpose, should one say "I did X ..." or "My advisor and I did X .. "?

This is an XY problem. Saying "I did X" repeatedly is wrong and offputting, and saying "My advisor and I did X" repeatedly sounds weak and annoying to read. Neither is the right option alone.

You should adjust the phrasing so that subjects are simple, mostly either "I" or "we", and explicitly credit yourself for things you actually did on their own. After all, you did have some independence, right? It's not like your advisor was over your shoulder every minute of every day.

Bad example:

  My advisor and I were looking for a project in field X. My advisor gave me a project to apply X to Y, and my advisor and I planned the general strategy after my advisor taught me the basics, so that after two months, some progress was made, though my advisor decided that the data analysis would have to be redone. Later, a paper was drafted with the editorial support of my advisor, which is now, after having been submitted, under review, at Journal Y.

Better example:

  I wanted research experience in field X and approached Prof P, who agreed to be my advisor. My project was to apply X to Y, and after a brief reading period I began two months of independent work, during which I picked up techniques A, B, and C. However, I found these techniques were not powerful enough for the problem at hand. We decided on a change of strategy, and I modified the analysis with techniques D and E, which I used to produce compelling results. We have written up and submitted these results to Journal Y.

Of course you would use fancier language in the real thing, but note how the second example makes you sound like an actual sentient human being, while the first makes you sound like you were just passively "along for the ride", even though it technically makes the exact same claims.


Is it impolite to not reply back during the weekend?

No it’s not rude, it’s called boundaries and you are allowed to have them. Simply because you are online and doing something else does not entitle anyone else to your response. There’s some nuance to this though, depending on your relationship to the person emailing, but boundaries can and should be established.


how to deal with this prof when he gives you his lowest grade?

You should assume the grading is fair, unless there is a reason to believe otherwise. Based on your question and comments, I don't see any reason to believe that discrimination is involved.

You state that you did everything that was required, just like the other students. That doesn't mean you should get exactly the same grade as them. Perhaps your presentation was not as clear as the others or your project had some minor flaws. It is very hard for you to judge that yourself -- you are neither an expert like the professor is nor objective in self-evaluation.

You received a 92, which is below the class average of 94. To me, that still sounds like a good grade and you shouldn't be concerned. Trying to argue for every last point is not productive -- it's called grade grubbing.


One Extra Semester - Benefits? Trouble Planning

I would recommend eliminating the philosophy major in order to start your graduate degree in mathematics sooner.  It seems to me the philosophy major does little to advance your career goals; you described it as a hobby.  Taking an extra (presumably fall) semester to graduate will delay your career by a whole year because graduate admissions typically only occur in the fall.  The year you lose comes at the end of your career, when you will presumably have the best and highest paying job of your life, or can retire a year earlier.  On the whole, the costs of an extra semester seems very high compared to the benefits.


Does anybody know why some journals have "Topical Collections"?

These are just ways to allow folks to find articles of interest within larger (less focused) journals.

Good examples are topical collections within a larger Mathematical Biology journal like the Bulletin of Mathematical Biology that correspond to subgroups within the society: https://www.smb.org/subgroups/

I think this will become more and more popular as journals get broader and broader.  Think about a journal like Nature Communications that takes science from any field... it's hard to 'browse' this journal in the way that you might browse a journal IN YOUR SUBFIELD, because the vast majority of the stuff is completely unrelated.  In a topical collection however, you might find things of interest.


Best strategy to learn programing for graduate research data analysis in biology

The best tool to learn depends on the actual job. For very basic data analysis, Excel has the lowest entry barrier, but the learning curve gets steep soon. Learning a full language will take some months, but will greatly expand the things she is capable of doing. Also, knowing programming in a field where everybody uses Excel can be a great advantage and unique feature for employment.

One important factor deciding which language is the environment she is in. Having people used to the tools and perks of a language can be very useful when learning from scratch. On the other hand, I'd only count "modern" options (some old professors are very fond of FORTRAN77 and IDL, but learning these is like learning to train dinosaurs).

She should consider not only her lab, but also ask at the Bioinformatics department, and take a look at other labs in the branch she is in. In my experience, for the most informatics side of the field, people use mostly Python, C++, and Java for some machine learning. I have encountered some MATLAB, but definitely not much.

One last note: I think in learning your first language you want the cleanest and less quirky possible. MATLAB in this respect is a mess of a language, with a crappy syntax and bad scalability. My personal choice would be Python, so here are some introductory materials:

Summer school on scientific programming and introduction to Python. All materials are posted.
The official tutorial. There is a lot of things that are not for useful for scientists, but it is very good introduction to the language.
Khan academy. They have everything. Very nice.
Coursera has a full assortment of courses. She will surely find something of interest there.


Can I consider this email from potential PI as a rejection?

It depends on what you mean by rejection. It's pretty clear that they are not willing to take you into the lab at this moment, but it's not a firm no. My read is that it's politely interested without being committal. I read it as follows:

The professor gave you specific feedback about your e-mail, suggesting they took the time to actually read what you wrote to them and consider you seriously as a candidate.

The professor says that they'd be interested in putting together a proposal with a longer deadline - this could be honesty on their part that they simply don't have the bandwidth to co-write a proposal with a short deadline.

They also suggest you contact a young faculty in their department. Depending on the department, this new faculty could be in the "orbit" of the bigger name, meaning that the big professor could see this as a way to keep you on the hook even though they don't have the funds to commit to you at this exact moment.

The professor didn't ask you for an interview or any follow-up. This suggests that they don't see it as even a remote possibility that they could take you on at this moment. They're then putting the ball back in your court. If you respond that you'd be interested to work on finding a fellowship with a more distant deadline, they sound like they'd be willing to move to the next step.

Whether you're in a position to wait a year (and probably two, since it will take time for your fellowship proposal to be reviewed), and whether it would be worth it for a shot to work together with this professor is something only you or those with more specific knowledge of your situation can answer. But, if you're interested in following-up, I agree with @henning that a suggestion of a phone call or video chat would be very instructive. Either you will get a good or bad vibe from them on the call, or their reaction to the suggestion ("sorry, i don't have time") will help you clear things up.


Are there any open access databases of all (or close enough) academic papers ever published? (not full-text)

I suppose you mean databases that are free to query so that you get to see all metadata stored without any subscription (i.e., not Scopus or Web of Science)?
Yes, there are various free platforms of that kind. My favourite (cross-disciplinary) ones are:

LENS.org (my favourite one - very comprehensive, and allows additional analyses and visualisations)
Microsoft Academic (not bad, powered by a semantic search approach)
Google Scholar (probably the most prominent one)
Semantic Scholar (another semantic search approach)
ScienceOpen (not too familiar with it)
CrossRef Search (only offers metadata about articles that have a DOI registered at CrossRef)
Wizdom.ai (offers interesting analyses, e.g. regarding research trends and grants)


How to treat papers or other work from dyslexic students?

The disabilities office at my Univ (large state univ in the U.S.) strongly advises that instructors not attempt to improvise accommodations for students with disabilities, whether self-declared or documented through the disabilities office. Their point is that we (outside the disabilities office) are not at all experts in such things, in the first place. Rather, the disabilities office will discuss with faculty the possible sensible accommodations, and in effect negotiate something. Faculty should not "get creative" and take initiative.

A significant point is that, although the circumstances or environment or timing or... for exams can accommodate, there is apparently never any notion that the grading rubrics should accommodate. That is, it's absolutely not that lower standards are applied to the output, but that the situation in which the output is produced can be modified. Indeed, it is not that we expect less in such cases, after all!


Is it standard to include a photo of yourself in a CV for a Swedish job search?

Swedish Wikipedia does not mention a photo: https://sv.wikipedia.org/wiki/Curriculum_vitae

This website mentions that a picture is not required in the cover letter and does not mention the issue at all in CV: http://www.yourlivingcity.com/stockholm/work-money/living-sweden-swedish-cv/

No pictures at https://www.cv-mallar.se/ or https://akademssr.se/dokument/cv-exempel

From nearby countries, photos are not be assumed in academic settings in Denmark, Finland, or Norway (based on personal experience). They do seem to be more prevalent in German-speaking countries, which do have close cultural ties to the Nordic countries.

Overall, it seems that a picture is not required, but, according to a comment from xLeitix, it would not be unusual to have one.


Am I allowed to use draft chapters of an early version of a book this way?

That is up to the book publisher. Some will be fine with it, others not. Copyright might be one (blocking) issue. If you have given up copyright to some conference, then some publishers will reject your proposal, since they want to hold it and it is no longer yours to give. Lectures and such are no real issue, since you retain copyright.
Another thing that might influence a publisher (around the copyright issue) is how different the book chapters are from the earlier material. But even then, you have to be careful about self-plagiarism since "repeating yourself" in one paper of something in another needs to be handled delicately and with full disclosure.
Just make sure you retain rights (possibly a license) to anything that you publish and want to include in a book later.
You can, of course, publish many things on a topic in conference papers that don't conflict with any rights that you might need in order to publish a book.


Did the professor "give" me this project?

It's research. You set out to build a plane and end up with a space ship. Or a glider -- most often a glider. If you were my student, I wouldn't say "I gave you the problem". I would probably say that I started you on a research direction.

Two years ago, a friend of mine gave me an idea and I tried to follow it. His idea seemed to lead nowhere. At some point, I read some paper I found by accident and found a way to continue his idea that he most likely couldn't have thought about. I did calculations and wrote a paper about it. Because he gave me the starting idea and constantly provided feedback and suggestions, I put him as last author on that paper.

Usually, advisers get authorship that way. In other words, they start you on a problem, and as you progress, they try to guide you and suggest you resources that could help you. You do start with their idea, which is often wrong, you do the work, and get something that is new. If it comes to authorship, some think that it's enough to get it if they just proposed the problem to you and did nothing else. I think that's not ethical, but it's hard for a student to enforce ethics.

The situation is different if the adviser has some strong indication of what the result of the proposed problem should be. That means he already did some work on the problem and needs you to finish. Then he deserves authorship even if he does nothing but point the problem out to you.

So, "giving the problem" and giving you a direction to work in is quite different. In the first case it's like you're a miner, and your boss tells you to continue digging a given hole because there's gold in it. You find the gold, he deserves a cut. But suppose he tells you to dig a random hole. You find no gold, you move to another hole, and find it there. He doesn't deserve a cut in that case, but he deserves thanks for letting you know that digging in a hole might lead to gold.

If it was business, the professor would get nothing beyond thanks, because they usually say that ideas mean nothing, it's only the implementation that counts.


Asked to combine work with competitors, but competitors are under ethical investigation

If there is any kind of ethical problem with the other group, you need to avoid involvement in unethical behavior as much as possible.  Tell the editor that, owing to ethical concerns, you are no longer willing to work with the other group.  You can ask them to consider publishing your work separately, but you should be clear that you would prefer to take your work to another journal instead of combining the manuscripts.


Are Graduate Fellowships or Research assistants in state university considered a government employees in US?

It likely depends on the source of the funds. If you were paid by the department at a State university, then the likelihood is that it is a Yes. But if you were paid through a grant then the answer might be no, but might depend on some things.
I suspect you should ask the department, or, alternatively, answer Yes, but qualify it somehow/somewhere with the actual arrangement.
But, as Paul Garrett notes in a comment, things vary by state.


How to phrase omissions correctly in a thesis?

You could explain one case in detail, then cover the other cases by listing what terms to substitute for the other cases. Especially if you're dealing with applying the same equation with different terminology, you could provide a table of which variable is named what in each case.

E.g.

  Because the principles only differ in terminology, only the solid to liquid transition is covered in detail. The equivalent terminology for each transition is in table 3.


Relevance of computer science degree to pursue a career in cognitive science

Think further ahead: what do you want to do after you finish the Cognitive Science degree?

Do want to go into academia and work as a professor (probably after some research postdocs) in the field? If that's your ultimate goal, then that's the most straightforward career path.

If it's something else, figure out what the prerequisites for that thing are. There are too many people who got into grad school pursuing a degree in something because they thought was cool only to discover that after they graduate, they have nowhere to apply their degree.

Whether it's worth it depends on you. Weigh the costs to you against the benefits to you.


I think you clearly sensed the concern that the interviewers might have with a candidate who is capable but seemingly unfocused. PhD completion rates are fairly low and one contributing factor is the motivational slump that occurs after a couple of years with very little light at the end of the tunnel. One way (that committees try) to avoid these unfortunate scenarios is to select candidates that are intrinsically motivated by their topic: whose passion for the subject itself will sustain them through the bleak slog that is methodology.

The problem is basically that, as you say, if someone held a gun to your head you could commit, but your advisor is not allowed nor obliged to do that. You need to decide independently whether you are honestly, deeply motivated by the desire to tackle hard problems (and make very little progress) in your subfield.

If it is the case that complex event processing in finance really is the field that will get you through years of low pay and minimal recognition, then you could send a follow up email along the lines of "Thank you for your time. I appreciate your consideration. Upon reflecting on our interview the other day, I feel I may not have appropriately conveyed my interest in SUBFIELD_X, which I think is important for VALID_REASON_Y" However, you should not be terribly surprised if this doesn't dislodge a negative opinion.

Edit: I should of course add that in many, many cases the specific (METHODOLOGY x SUBFIELD) that you are deeply passionate about today, will not ultimately be the one in which you complete a thesis. This is okay, as long as the passion carries over.


Conference fee and travel costs for invited speaker

The larger and more prestigious the venue, the higher the probability that your conference fee and travel costs will be paid by the venue.  Certain invited speakers (particularly keynote speakers) will also be given a speaking fee, but "invited speaker" means different things in different venues.

You should, therefore, explicitly ask.  First, if it's a small and not well-funded venue, they may be asking for you to volunteer rather than offering to pay.  Second, many predatory / scam conferences send out official "invited speaker" invitations that attempt to stroke your ego and get you to give them money.

If you don't already know the people and the venue, be careful because it is quite likely to be a predatory / scam invitation.  The "invited to present a published paper" is a particular red flag, as these venues seem to have a semi-automated method of scraping publication databases and inviting authors to give them money to talk to a half-empty room of others who have been similarly scammed.  Once you've published a few papers, you'll get a lot of these---I get several per day.


Timely answers to academic e-mails and internet addiction

What's considered a timely response depends on context.  A response could be expected within hours, days, or weeks, depending on the email.  What I think is important is that both parties are clear on expectations.

For normal academic activities, I would say checking emails twice a day is generally sufficient.  Academics are often busy with classes and meetings throughout the day, so it's generally understood (at least between faculty, though not always by students) that you might not read or respond to an email within an hour.

However, it sounds like your PI expects you to check email more frequently than you do, so it's probably worthwhile mentioning that you only check email a few times a day (if asked why, just say so it doesn't distract you too much from your work).  Then you can see if your PI is happy with calling you or seeing you in person if it's something urgent.  If not, and PI really wants you to check email constantly, maybe you can set up something where you will only see emails from your PI (e.g., forward them to another email that you use for nothing else).

Similarly, if there are other people that seem to be expecting immediate responses from you, just maybe add a "PS" in your reply about how often you check email.  I don't think most people will be upset if they know your habits.


Colleague's grant application resembles my PhD thesis

I suggest three things. First remind him of your dissertation and send a link to it, noting that there is similar wording that might become an issue. Second, I would, under the stated circumstances, offer to help in the application. It seems like it might be an attempt to extend your work, rather than to plagiarize it. That is always appropriate. And you could also assure that you aren't plagiarized if you are in the loop throughout.

But, if you have the time and energy, I suggest that you offer to be a consultant on the grant as it progresses. This would get you named specifically in the application, at least. Your actual participation could be minimal, or not, but you could at least see how the work progressed and get more involved as time went on. It might not be impossible to be paid a bit for consulting work, depending on the agency and its rules. Consultant on a grant is a CV line, if nothing else.


Can section numbering depth exceed table of content depth in thesis?

Is this OK or is there some convention that says you have to have the same numbering depth in your table of contents and text?

There is no general convention against this, but your supervisor or university may hold dogmatic views on it, so you have ask them or read their regulations, respectively.

That being said, the question whether it’s a good idea can usually be answered best if you consider the purpose of the respective elements:

The purpose of the table of contents is to allow the reader to quickly find a specific part of your text and to give a rough overview over your structure. You do not need a certain subsubsection or similar in your table of contents, if both:

it is safe to assume that everybody who is looking for the contents of some subsubsection or similar will find them as well if it is not explicitly listed in the table of contents;
the subsubsection is not essential to your thesis’ structure (which is very likely).

Actually, I think that many theses do not need a table of contents that goes beyond the first level.
The purpose of having subsubsections (and similar) is to structure your text and to be able to have precise references within the text (e.g., “see Sec. 4.3.2“). Thus a subsubsection is not needed, if both:

You do not specifically reference it.
It does not help the reader to see how your content is structured.


Counter strategy against group that repeatedly does strategic self-citations and ignores other relevant research

First, I think it's important to have a more precise diagnosis of the problem.

Self-citations by themselves are not necessarily a problem---even 30% self-citations might be quite reasonable depending on circumstances (e.g., work in a very narrow but deep niche).  Likewise, re-inventing a result is not necessarily a problem if the prior result is in another community and your community was genuinely unaware of it.

Failing to properly credit the work of others when made aware of it, on the other hand, is definitely a problem, and can be addressed by the community of peers:

For journal articles, the peer reviewers can simply insist on citations.  It's very easy to add a citation in revision and pretty much never a reason not to cite closely related work.  Furthermore, reviewers get to see it again and don't have to say "accept" until they are satisfied. Thus, unless the editor thinks the failure to cite is OK, it's easy to force the citations to be added as a condition of publication (or they can go to a crap journal instead, which is worse for them).
For conference papers, it is more difficult to insist on citation, since there is often no second round of review.  Here, I would recommend invoking the ongoing pattern of failure to cite in a review as a reason for giving a low score, thus signaling that this does not appear to be an accidental oversight.
For slides, of course, there is no pre-presentation review, but there are post-presentation questions. "I notice that you failed to mention Smith's prior work on this problem, would you care to comment on its relationship to your work?", "How does your results compare to Xu et al's results on the problem?"  Embarrass them in front of the peers, and they will be motivated to improve---and more importantly, the peers will be motivated to make the same requests.

None of these strategies are things that you can really do just by yourself. But if it's a legitimate issue (as opposed to, for example, a potential distorted view of the significance of your own work), then other peers will hopefully have noticed as well and can be doing the same.


Tutoring is definitely a great way to gain more confidence and knowledge in a certain area as well as help you to decide if you enjoy the subject/teaching it and want to go to grad school. However, it sounds like you know the class really well as you received an A+ and it isn't worth dropping a lecture just to tutor. Grad schools do not put nearly as much weight on tutoring to warrant sacrificing other things that would benefit you.


Rejection of a job offer in favor of another. Is it worth trying to fight back for the first one?

It could never hurt to contact job #1. Maybe they will still need you. I would recommend that you avoid telling them that you are only applying to them because another job rejected you. People do not like being the fallback plan. Simply explain that with more time to consider your options, you came to realize that Job #1 is an excellent opportunity and that the move/distance from you current location should not be a barrier to pursing the important opportunity with #1.

Understand, of course, that they may have already filled the position with someone else. In that case, all you can do is move on.

p.s. Never deal with people who renege on agreed to terms of employment. That should never be tolerated.


How to tell my MS advisor I've changed my mind about doing a PhD with him?

Two points:

First, just because your new supervisor offers you a PhD position does not mean that you are in any way obliged to take it. That said, don't hide the fact that you are going to consider sending applications out to a variety of programs. The thing that will cause hard feelings is if your advisor thinks you are going to join his or her group and turns other people away, only to have you leave. If your supervisor is a professional, he or she will recognize that you pursuing other opportunities is not personal. You have to do the best you can for your career, and if that means taking a better position elsewhere, then you should do so. (Note that you can also get outside offers and use these to negotiate better pay as a PhD student, but that's a different issue, and somewhat more complicated politically.)

Second, don't under any circumstances work for a group that makes you be slow and do poor work. Academic hiring is cutthroat competitive, so if you want to actually get a job, you're going to have to produce a lot of very good work, and you're only going to do that if you're surrounded by other people who are trying to do the same who push one another.


How long typically are paper reviews? Is there such a thing as “too long”?

Speaking from the point of view of an editor: One of the best reviews I ever got was longer than the paper. The author, a young researcher, had proved three theorems, one of which I recognized as a known result. So I asked the original discoverer of that known result to referee the paper. In my cover letter, I mentioned that I recognized one of the theorems as his, and asked whether the other two theorems had enough novelty for a publication. It turned out that the other two theorems weren't new either. The referee could easily have just given citations for those two theorems and recommended rejection. Instead, he gave me (or, really, gave the author) a long, clear explanation of the state of the art in that subject, and he suggested some open problems that the author could try working on.


Is it appropriate to rewrite and republish another author's useful but very badly written paper?

Personally, I would be very happy to read an abstract along the lines of

  ABC is an important problem because of XYZ. A solution to this problem was presented already by UWV et al., but is not widely known, partly because of the technical nature of their presentation. Here we give a readable presentation of UVW et al.'s ideas, showing that they can be interpreted in terms of PQR, and we give applications in the field of JKL.

If the paper is mostly a reinterpretation of existing work it might not get into a top journal, but if the problem is important and the solution is a good one, your paper will be a valuable contribution and is likely to be widely cited anyway, since most people implementing it will be working from your paper and will cite it along with the original.

There is no danger of it being seen as plagiarism if you are presenting their ideas in your own words, and state at the start that this is your goal. The other authors will likely be happy as well, because their work will become more widely known as a result of yours. There is no need to involve them directly at all, although of course this is possible as well.


How did Russia produce a comparable COVID vaccine with inferior resources?

Ranking or spending money is only secondary metrics how to evaluate and compare performance e.g. among universities or countries or continents.
But I think fundamental is society, it's history and its attitude. I had opportunity to live and experience research in "western" country institute for couple years. This experience may apply to general research as well as to hunting vaccine competition:

Oh your idea is great, let try and start
we give you some time and administrative support to enhance the idea
big pharma as well as small startups are close to university labs, so it's not hard to do quick experiments, trials, prototypes. Some networking events, conferences are common.
you're good in what you're doing, we're among the best in the world

Now back in "central & eastern" european country usually underestimated. I now experience this attitude:

Oh your idea is interesting, but somebody (from western countries) already works on this issue
administrative support? Write proposal by yourself and we will only evaluate if the 'quota' was not reached so you won't compete with "more preferred" teams.
usually big pharma or small startups are not close to university labs - if yes, that is "conflict of interest" and you "try to sell knowledge to nasty rich companies"
there are better teams in the world in the topic doing what you do.
you did unappropriate public critical comments about our dean, prime minister, president, ..., so forget for support

So as a result I can guess that in countries and societies from first group ("western") there are e.g. 20-50 teams trying different approach despite their political or other context. 2-5 succeed, the others that fail - they are not usually prosecuted but gain valuable experience. Some earn money and pay taxes, some become rich and invest again to western business and all society in general profits.
I guess that in countries and societies from second group ("eastern") only 2-5 teams try to make  vaccine, other were disqualified by any point mentioned above. If 1 succeed despite condition - it is big success! Congratulation to Sputnik V! They earn money, probably pay taxes, some become rich and invest where? Do they rather to emigrate to west, not to be imprisoned like Navalnyj or Khodorkovskij? What about the other teams that do not succeed - are they prosecuted?
So in case of western approach - the luck is just statistical success rate.


How should I select the correct path for doing my higher studies

For physics PhDs in the UK, the minimum requirement is a 2:1 in your undergraduate degree, which you have (I say physics specifically because that is what I have experience with). However, applications are so competitive that you usually need above the bare minimum to be considered. This means either having a better grade in your undergrad or doing a Master's degree.

My suggestion to you is apply to both MScs and PhDs simultaneously. Then, if you get accepted to a PhD, great; if not, then do the MSc and apply for PhDs once you've done that. Good luck!


I know from all too personal experience that it the easiest thing in the world to say "I could totally ace these assignments if I tried, but I can't be bothered to try." Talk is cheap. You may be different, but when I said stuff like that I was completely deluding myself.

You may be being too hard on your profs and TAs. CS departments generally don't cover specific development platforms in their classes because platforms come and go, sometimes in a shockingly short period of time. A good CS department is going to try to educate you in the foundations of CS and software engineering. Stuff that is not in the tech headlines now, but is more likely to still be relevant 10 years from now. Still, it may be that they aren't very good, in which case the solution is not necessarily to drop out, but to find a better department.

That said, if you aren't applying yourself in school, and aren't getting much out of it, then you probably should't be in school. However, if you are not going to be in school, you still have to move forward with your life. You can't just hop on the bus back home and let your parents support you. The accelerator sounds great, but it's a roll of the dice, so you need a backup plan. The obvious choices are joining the military and finding a job. I've never been in the military so I can't advise you about that. If you find a job that pays all your expenses, then your parents may be upset, but they can't really stop you. They probably will be less upset with you if you have a job in hand as you announce that you are leaving school. If you can't find a job that will support you, then that's a pretty critical piece of information, and it means you've either got to suck it up in school or join the military.

My suggestion would be to completely put aside your personal projects for the rest of the year. Focus on your schoolwork, and prove you aren't just blowing smoke, when you say you could excel at it. Prove it. At the end of the school year, start looking for a job. If you find a job that will pay all your living expenses, or if your accelerator works out, then take a leave of absence. If you prosper in your job or startup, great. If it doesn't work out or seems like a dead end you can go back to school. If you really want to pursue your projects as an entrepreneur, then live on Ramen, save every penny, and bankroll yourself for a couple of years.


Wiley
Taking a look at Wiley’s general copyright agreement, they only “the Contribution”, which in turn is defined in the header as “Manuscript entitled ___”.
Now it’s debatable whether the supplemental material is part of the manuscript. However Wiley needs at least some permission from you to publish the supplemental material and I could not find any information on separate copyright agreements for the supplemental material, so I assume that at least Wiley considers the supplemental material to be included in the manuscript.

Wiley-Blackwell licenses back the following rights to the Contributor in the version of the Contribution as originally submitted for publication:
a. The right to […] place in a subject matter archive, […]. This right extends to […] the Internet. The Contributor may not update the submission version or replace it with the published Contribution. […]

Again, it’s not specified whether this applies to parts of “the Contribution”, but given that a partial publication is less than a full publication in terms of copyright, I would argue that it’s included.
Finally note that all of the above only applies to the general copyright agreement. Wiley mentions that the individual journals may have differing agreements:

Author re-use rights vary between journals. Please refer to the copyright form you have signed or are required to sign to review the applicable re-use rights.

As there are some questions of exegesis in the above, the easiest safe way is to ask Wiley whether they agree with your endeavour.
In General
Addressing the titular question:

Do journals have legal copyrights to the online supplemental information?

As journals want to disseminate the supplemental material, they need you to at least transfer at least the rights needed for this. Since those rights are a subset of the usual copyright agreement, it makes sense from the journal’s perspective to plainly treat the supplementary materials the same as the main paper:

It’s less complicated for the reader.
It’s less work.
Most people do not care much about supplementary materials anyway.

Therefore I do not find it surprising that most journals (in my experience) do this. However, at the end of the day, you have to look into the journal’s copyright agreement to be sure, or even talk to the journal itself, if the copyright agreement is ambiguous and you do not want to risk any bad blood.
Finally a sidenote from personal experience: I once wrote a paper presenting a new method and wanted to attach the source code for an implementation. Since the journal’s copyright agreement did not allow me to disseminate the source code on GitHub with a free license simultaneously and the copyright department did not want to relax the copyright agreement in that respect, I ended up removing the supplementary material and posting it on GitHub alone.


Can version control systems, like Git, be used to establish priority date of a paper?

I understand your question in the following way:

You are asking if a git repository can be used to add a "timestamp" to some idea, so that in case multiple researchers come with the same idea, you can prove that you were the first (whenever this is actually true).

Unfortunately, dates in a git repository can easily be forged. See here for a stackexchange thread documenting this.


Is it acceptable to wear the same outfit every day?

One of my faculty colleagues who just received tenure (at my r1 university) has worn basically the same outfit (same colored button-down shirt with khaki trousers) for the past decade - from graduate school to his current position (he may have indeed been wearing this his entire life, but we only have data for the past decade). I believe his closet only has one type of shirt and trousers.

Aside from gentle ribs from others about his 'uniform', it's well tolerated by others as it's a minor eccentricity compared to some of the other faculty.  Just be open to someone asking you if you: 1) have multiple shirts or a single shirt; 2) wash them regularly.

tldr: If it saves you money / brain-cycles  / spoons / closet-space to wear the same uniform clothing every day, do it. It worked for Steve Jobs, it can work for you.

Fine print: There may be a gender factor as men in academia and industry who basically wear a uniform are well known but it is rare to encounter women who do the same. This requires more exploration.


Is it advisable to attend a conference in Germany with talks by German presenters in English if you don't speak German?

Here are some claims that I think you will agree are true:

Anyone who attends a conference where all the talks are in English can understand spoken English reasonably well
You don't live in Germany and are considering attending. You are probably not the only person considering it
Anyone willing to give a technical presentation in English can probably both understand and produce spoken English reasonably well

I believe these add up to you being able to find people for "hallway conversations" in English pretty easily. You might have some lonely lunches if you find yourself at a table with people who all speak German and exclude you. I have this problem with people who all discuss (in English) something I don't understand at all and don't want to learn (eg how to install Exchange on a server.) I generally try to prevent this by striking up a conversation with a fellow attendee at the end of the session that is right before lunch, and suggesting we go to the lunch line together.


It's probably worthwhile to mention it:

Pros:

If you work in a related field, this could be used to demonstrate
that you are a good candidate since someone is prepared to pay for you
because they think you are a good catch.
It is also more generally not bad to show that you are a competitive
applicant who has attracted awards for past performance.
Finally, it suggests that you are serious about pursuing your Masters (have secured your own funding or at least will not be deterred by financial issues). That could also be helpful to the admissions people if they are concerned with acceptance rates into the program.

Cons:

If the program has its own scholarship/funding you might take yourself out of the running for that and be committed to returning to work for your company after you graduate because you have used their scholarship.


Can I reduce/change the margins given in the template of a journal?

The entire point of the template is to make certain that everybody is on the same page (no pun intended) as to what the format is. Changing it defies this purpose and will almost certainly be noticed – if the journal uses this template for production at all.

While nobody except the journal staff knows how exactly they would react to what you intend to do, I would prophesy that at best they directly return the manuscript to you and ask to properly shorten your manuscript.


Is there a lot of writing in PhD programs in top-rank US schools?

Yes, you should expect to do quite a bit of writing as part of your courses in any high-rank U.S. university.  It is, indeed, good practice, and in a good university your work should indeed receive significant scrutiny and feedback from the instructors.

Furthermore, I would not be so quick to dismiss such practice in technical writing.  First, the quality of prose that you have produced in the initial version of this question clearly indicates that you have a long way to go before you can routinely achieve a high professional standard of writing.  Second, no really good writer ever considers their art to be finished, and that includes long-experienced academics.

Do not forget that communicating your technical work effectively is just as important and difficult, if not often more so, than doing that technical work in the first place.  I know people who have run their careers into the ground from a reluctance to invest sufficiently in becoming comfortable with scientific writing.

In short: if you want to be a scientist, you've got to embrace the writing.


How and when to cite code from MATLAB File Exchange

This answer is from my own personal experience in academia and may/may not be strictly SOP, however, I'll do my best to answer.  Most of this is assuming that you have not drastically altered the original code for your work.

1) FEX submission is clearly code from a paper written by the same person.

In this case, contact the person and let them know you are using their code in your work, cite their paper, and acknowledge their code in the paper.  This is especially important if their code was critical to your work.

2) Code is from a paper, but the author of the code is not the same author than the paper.

Cite the original paper as it is providing the basis of the code that you are using.  Contact the author of the code and acknowledge them.

3) Code is a nice tool, but has no available citation. E.g. inpaint_nans, nice tool to fill "missing" data.

This is an example of when the code doesn't accomplish the goal of the research and is therefore not going to be mentioned in the paper.  In this case, you can acknowledge the author in your own code/ software, but not in your paper.

4) Code that is a nice tool, someone coded it, but its little effort to rewrite as it's not a complex tool. Still, someone write it and, time==gold!

In this case, it is probably not even worth any mention.  I think everyone on the exchange understands at some point, contributions are designed to further programming itself, not themselves.

5) Code that is a nice tool, takes little effort to rewrite, but its code referencing more than one paper. E.g. 3D Shepp-Logan Phantom, references 2 papers, and its a short function.

In this example, this code is copyright protected but also released under GPL. Follow the procedure for GPL and when in doubt, contact the author.  If the code is central to your work, acknowledge the author at the end of your paper.

Summary: If the code is central to your research theme, contact the author.  If the code is a tool that 'fills in the blanks', it doesn't need to appear in the paper, but should be referenced in your code.


As far as I can see "member" has developed everything from idea to finished product. There is very little sign of anyone else being involved other than possibly as a discussion partner at the lab. To allow someone to use the idea still does not take away the intellectual property held by the member unless there has been important feedback from someone. So I would not hesitate to try to move forward towards publication with the idea. I simply cannot see any ethical issues based on the details you have given.

Having given the green light, there will always be the issue of personalities. You allude to some level of conflict in terms of the move by the member. It is not inconceivable that the PI may have a different view and this view may not even be anchored in reality. So even if you do everything by the book and have all rights, that does not preclude the PI from doing all the things you express, it really depends on the PI's personality.

In the end member should think through if anyone has contributed to the work to the degree that merits co-authorship. Member can, for example, use the the post What are the minimum contributions required for co-authorship to set the authorship in perspective.


How to cite a statement that cites several other sources?

One approach is to cite Gareis (2010) as the source of the other citations:

  According to Gareis (2010), many international students complain about a lack of meaningful contact with host nationals (cited by Gareis, 2010: Gareis, 1995; Klineberg & Hull, 1979; Marginson, Nyland, Sawir, & Forbes-Mewett, 2010; Ward & Masgoret, 2004; Yashima, Zenuk-Nishide, & Shimizu, 2004).

If you use this approach, then you need to include ALL these in your References list (a.k.a. Bibliography).  In this case it would be 6 references total.

This approach is most useful if these specific sources are important for your purposes, either because they establish credibility, present details, or make important connections to lines of research or results.

Another approach is to omit the specific citations by Gareis (2010), but also to note that you omitted them.

  According to Gareis (2010), many international students complain about a lack of meaningful contact with host nationals (five citations in Gareis, 2010 omitted).

This approach is most useful when you only need the main citation as support of the statement and the specific citations are not useful or necessary for your paper or for the reader. In this approach, you'd only have one entry in your reference list for Gareis (2010).


How to deal with a guilty feeling after graduating with very high grades as MA student?

It is not inherently unethical to "recycle" previous coursework.  It is only unethical to do so without the current professor's knowledge.

Professors may determine, based on their own teaching philosophy and the circumstances of the course, whether or not it is acceptable to reuse work completed for previous courses.  In this case, you told the professor and he consented, so obviously he decided that reusing your previous paper still met the academic standards he set.  Someone else who learned about the matter might have a different opinion, but they would respect the decision he made.

Your actions in this case were completely ethical.  There is no way they would lead to future academic dishonesty charges, let alone a revoked degree.

As for the semester abroad, your transcript will clearly show that those classes were taken at a different institution.  You'll provide those records as part of applying for a PhD, and the professor or committee considering your application will be able to consider them in context, taking into account their own opinion of the standards at that institution.  Again, everyone has complete information, and there is no deceit or unethical behavior.

As for the academic distinction, it seems pretty clear to me: your institution had criteria for awarding the distinction and you met them.  In setting those criteria, they certainly would have taken into account how to consider coursework completed at other institutions.  So again, no deceit.

Anyway, I am not sure about Europe, but in my experience, such honors are pretty meaningless in practical terms.  It will look nice on your diploma, but someone evaluating you for a PhD is not going to look at what distinctions you may or may not have received; they're going to look at what you actually did.  So it's fairly pointless to worry about whether or not you "deserved" something that, in reality, doesn't convey any practical benefit.


Food for comprehensive or qualifying exam?

My question is, how often do students do this for qualifying or comprehensive exams?

At my previous department (in ECE, if it matters), students do for qualifiers/prelims what they do for their defense, the only difference being that you scale down the total quantity of refreshments that you provide/purchase a bit if the exam is not open to the public.

  Would committee members expect at least some coffee?

I don't know about "expect," but it's nice to have some on hand: at all of my exams, all of my committee members went straight for the coffee upon arrival to the exam.

Edited to add — The oral portion of the qualifying exam at my previous department consisted of a presentation which was meant to showcase any research highlights the student had achieved up to that point and future directions. If your qualifying/comprehensive exam is like that described by @CameronWilliams below in the comments, then bringing refreshments may not make any sense, i.e. your mileage may vary.


How to protect scientific open research from being patented?

Legally speaking, any disclosure of an invention prevents it from being patented: it counts as prior art. Disclosure includes not only publication but also public demonstrations, as well as sales (except possibly when subject to a non-disclosure agreement). This is part of the novelty requirement of patentability.

There is an exception: in some countries, the inventor has a grace period after disclosure during which they can still file a patent. This only applies to the inventor, a third party isn't allowed to file a patent for something they didn't invent, or for something that somebody else has already published. The longest grace period around the world is 1 year, in the US. Some jurisdictions such as the EU have no grace period.

Thus if you publish your research, this protects from anyone subsequently filing a patent on it. Even if they had invented it previously, your publication would invalidate a future application. After publication, the only remaining risk is that you, or a fellow inventor who worked with you, take advantage of the grace period to file a patent in countries where this is possible. I don't know of a way for you to legally guarantee to others that you won't file a patent.

Note that you need to publish (or at least publicize — a private disclosure is sufficient to invalidate a patent unless it falls under the scope of a confidentiality agreement). If you invent something and don't publicize it, that allows someone else (presumably working independently, since you didn't tell them anything) to file a patent on their own invention. Being the first to invent doesn't bring you an advantage (it used to in some countries, but since the US switched in 2013, all countries have a first-to-file system). Fortunately, publishing open research shouldn't be an onerous requirement.

That's the law. In practice, patent examiners don't always find prior publications. The ubiquitous Internet has made it easier than it used to be, but conversely the increasing volume of available knowledge has made it more difficult to find the needle in the haystack. If a patent has been accepted by a patent office, it can still be contested due to the existence of prior art, but this requires a court decision, which can be costly.

Some research institutions (public or private) have a formal practice of defensive publications: publish potential inventions that they don't intent to patent as soon as possible, in order to block anyone else from patenting them. Technically, any publication is a public disclosure, including an arXiv preprint, a blog post, or even a research seminar if it's legally open to external visitors. However, since it's easier to fight a patent before it's granted, it is advantageous to make it easy for patent examiners to find the defensive publication.

If you're concerned about someone filing a patent on something you discovered, or for that matter anything that you know about, you can watch patent applications. Patent applications are published for a period of at least a few months, during which time anyone can point the patent examiner to something that they consider to be prior art. Stack Exchange participates in this process through their Patents site where people can coordinate prior art searches.


What to do if an audience member refuses to let you answer their question?

The question's title does not reveal the status of the obstructionist questioner, and this status matters enormously. Lower-status people behaving this way could not "get away with it". High-status people often can.

Given all the implicit primate-interaction and other presumption in anyone's behaving like that, in particular denying response, this should be treated like bad drivers on the highway, specifically, potentially more reactive than the indifferent bad weather or bad luck of various sorts. Namely, any substantial response, especially any expression of annoyance or umbrage, will incur a cost that makes whatever satisfaction one had hoped-for too expensive.

Instead, a dumb-happy-innocent smile and "thanks for your comment... then", to avoid engagement, is wise.

Sure, this amounts to a sort of impersonal bullying, but you yourself could not likely change the outcome. It'd require the intervention of someone of comparable status, blah-blah-blah.

So, in summary, no, such "comments" are not productive, are status-reiterating, ... and do create a generally stifling status-conscious atmosphere. Not that most human scenarios aren't status-conscious... :)


How to format ranges including negative values in tables?

Personally, I would definitely not use this type of formatting, as I think it is easy for people to confuse the various different types of dashes.  Instead, I would recommend using the bracket format typically used for denoting intervals. Formatted in this manner, your examples would be:

[-0.2, -0.14]
[-3, 3]


When applying for a postdoc, the contact person is not the professor I want to work with, what shall I do?

It's simple: follow the instructions. If the contact email address is of prof. B, then you should address him in the greeting.

Do not make assumptions such as prof. B is recruiting postdoc for prof. A, or at least you should not bring this assumption to your conversation with prof. B, even if your assumption is correct. Many people may take it as disrespect.


Is there an equivalent to journal impact factor for scholarly book publishers?

Thomson Reuters offers the Book Citation Index.

Interesting side note: I just found this publication by Kayvan Kousha and Mike Thelwall (2014) (posprint for free on ResearchGade) stating that Google Books is a good source for Book Citations, "despite  its  lack  of  a  public  citation index."


Should I explain to the graduate admission committee why I am older than most prospective PhD students?

Such information would be relevant. The real trick would be to keep such a paragraph short and to the point. As such the question would be a good draft of such a section. I have two comments:

I would not start the second sentence with "as you know". If a committee member did not know, you make her or him feel ignorant. It is good to avoid invoking negative emotions in such a letter. Especially since leaving that part out does not change the meaning of the sentence.

It was not clear from the text whether it was the Bahai faith that prohibited it's members from going to university or whether it was the Iranian government that prohibited people with the Bahai religion to enter university.


What are the steps I need to take when an author won't answer clarification questions?

I get far more emails than I can reply to, but occasionally I do reply to random emails from people I don't know concerning papers I have written.  The main factors that lead to me replying are: (1) I can see that the person is genuinely interested and has tried pretty hard to understand. (2) The person has a very concrete question that I can easily write down the answer to. (3) I am not overly pressed for time from other obligations.
In your case I cannot tell what kind of email you wrote.  But if it says roughly "Dear X, I am interested in your paper but I don't understand your data collection methodology.  Could you explain it in more detail?  Best regards, Y." then I would ignore it for sure.  Why?  Basically the person has written a minimal-effort email, and so I assume they probably read the paper with minimal effort too.  And what they want from me is completely unreasonable: They want me to write an expanded methods section just for them.
On the other hand, if the email would show a deeper understanding of the topic, and they would clearly explain their confusion and ask a specific question that I can easily clarify, then I am happy to do so, even if it takes a couple of paragraphs of explanation.  However, such emails are rare.
When you publish a paper, the paper stands on its own, with all its strengths and weaknesses.  A paper does not come with any warranty or guarantee that the author will freely provide all interested readers with further personalized instruction on the topic of the paper.


On the importance of an "honours degree" for PhD applications

Serving on a doctoral faculty for many years, typically when candidates are evaluated there are specific criteria that first have to be met. So, they will evaluate basic things like your GRE score, GPA, TOEFL score (if applicable). They will also evaluate your writing sample, if required to make sure that you will be able to write at the graduate level (use of references, clarity of writing, etc.).

Other than that, they will evaluate how well you fit with their program. Are you planning to study a topic that is aligned with the work already being done? Do they have an appropriate mentor/advisor to match you with? Do you express a sincere interest in research (our program emphasized research, but we would receive applicants who wanted a PhD and continue working as practitioners in the community. We weeded some of them out if it looked like they would not excel at research).

So, the Honors designation alone won't necessarily put you ahead of other candidates. That being said, if a doctoral program has a limited number of graduate stipends available, they may only accept the most qualified candidates - if the honors program you mention has specific coursework that is in strong alignment with the graduate programs you plan to apply to, then you may want to consider the additional study. However, if you have a strong record of the programs' requirements and write a compelling statement or writing sample, the honors program may not be your best investment. Best of luck!!!!!!


Mathematics Stack Exchange as an indicator for academic career

The only thing that a high MSE or MO reputation indicates is that a person spends too much time on the internet (and I say that as someone with a reasonably high reputation on MO).  I don't think you should take it seriously as a data point on how successful you are likely to be.

On a related note, it also doesn't play any role in things like hiring decisions.  At all the places I've worked, someone would be ridiculed if they brought up MO or MSE reputation at a hiring meeting.

It's just recreation.


How to stay motivated in a group with low motivation?

Flee or fight.

Flee is obvious. Fight means focusing on your goals and finding something rewarding.

I've experienced low motivation, I am at this precise moment suffering high temperatures and lots of noise, the work environment is very important and it will have a toll in your productivity (and your career) if it is not the right one.

The point is, either you leave to a better place (if possible, that depends on several factors) or if you decide to stay then you need to compensate from that toxic environment.

I read some time ago a blog post titled hack your motivation, which could be useful. In general what I find most motivating is keeping track of my progress, on a daily or even hourly basis, either writing a section of a paper, running/conducting an experiment, programming some class or complex method, or anything else. Anything that gives you the feeling of making some progress.

That's probably why your colleagues are wasting their time, games provide some fictional reward, some fictional and imaginary sense of achievement, games are like porn in that sense (no real sex, only fiction and imagination). What I mean, in short is: gamify your research. You all will be playing games, but you will be playing the right one (assuming you do the gamification right).

This site is a good example of gamification. I have 2093 points already! I would feel less sick with some A/C, though...

What you have to ponder are your chances in this flee or fight scenario. I can't tell you whether you will have more success running to a less toxic environment or reducing the toxicity for you. It depends on the opportunities that you can find to flee and how strong is your motivation and gamification to fight toxicity.

That's your decision and yours alone.


Good multiple choice question for education

You could probably ask this as well on MathEducators. To be clear, I haven't found any academic study about it, but even if there was one, you should know in advance what you are expecting to achieve.

I interpret your answer as in: "Should multiple questions allow options to be eliminated with partial effort?"

The answer of course, is that it depends a lot. Think carefully about:

  What kind of test are you preparing?
  Is this a regular exam for elementary school that accumulates points which eventually determine if students are approved for the next year?
  If so, and if questions are easy already, I'd go for the equal chance for each alternative.

Or are you preparing an admission exam?
In easy admission exams, every bit of knowledge should count, so that the guys who knows nearly nothing is ahead of the one who knows nothing.
In difficult/competitive admission exams, people who are to be admitted are limited in their score by their performance accuracy, not by their knowledge, and possibly by their speed. So these tests are designed to have very good students getting around 70% of the maximum score. I've known such tests to contain this kind of problem either to mitigate the effect of very difficult questions (you give an easy way for the student), or to give time to the ones who master the subject well enough to think how to approach the problem even if they know a standard (and time consuming) solution method.

  What average score should students get?

Again, If you are expecting bad students to get good grades, maybe you shouldn't bother to make it even easier, but if you expect good students to have bad grades, then why not?

  Are you evaluating effort or just results?

Maybe you are giving 3 absurd options and 1 reasonable 1. Maybe you are giving 4 reasonable options, but some of them can be eliminated with knowledge of the subject. The first case only rewards students for reading the answers, while the seconds can measure some level of knowledge on the subject. Makings options impossible to eliminate rewards the student for the effort of solving the question, this is well represented in calculation intensive questions. But if the question is simple and "you either know it or you don't" (think asking who painted the Mona Lisa), you can make eliminating options difficult.

So effortless question does not give much room for allowing options to be eliminated, but work intensive question do. IMHO.


For what reasons (if any) would a journal refuse to inform the reviewers about the final accept/reject decision?

One possible rationale would be a belief that the acceptance decision ought to be a confidential matter between the journal and the author, and the reviewers simply don't have a "need to know".
The argument "it is important feedback for the reviewer" isn't very strong, in my view.  Knowing the fate of the paper doesn't really give you much information about whether your review was helpful in reaching that decision, and certainly doesn't tell how you could have made it better.  Conversely, if the editor wants to give you feedback on your review, they can certainly do so without revealing the final decision.
By analogy, consider what happens when you write recommendation letters for people.  When they apply to a school or employer, the school doesn't tell you whether the applicant was accepted or not, because they consider it to be nobody's business except the applicants's (and privacy laws may back this up).  Of course this is a different situation in many ways, but I think the underlying principle is the same - having been part of a process doesn't, in and of itself, entitle you to information about the result which would otherwise be confidential.


How successful would one be in switching fields from PhD in computational biology/neuroscience to postdoc in computer science?

I believe that career changes and "reinventions" are a regular part of modern careers in highly specialized fields. Very few people will be able to work in a single domain for their entire careers, and the ability to move laterally between "adjacent" fields will be a critical skill enabling one to have greater chances and opportunities for success.

Now, that said, your chances of success in any particular job hunt will depend to some extent on how "enlightened" your future boss (or hiring staff) are: some will actively seek out anyone with the appropriate skill set and enthusiasm for the work, while others will be more focused on people who have the "direct" skills they need, assuming such people will require less training to be able to carry out their work. Neither of these positions is "better"; they just happen to coexist.


PhD in Management Science and a faculty position in CS

At least three faculty in my department (including our current head) have PhDs in electrical engineering, at least one has a PhD in mathematics, and at least one has a PhD in operations research.  If a faculty candidate is actively publishing good research in computer science conferences and journals, which department gave them their PhD really doesn't matter.  (And if they're not actively publishing good research in computer science conferences and journals computer science research, they won't get hired, period.)

Most junior faculty candidates don't have significant teaching experience anyway, so that aspect really doesn't matter much either.  Sometimes it can be a bit tricky to find courses for new faculty with non-standard backgrounds to teach, but if they're really doing CS research, something always fits.


What is a "full-time teaching faculty" (and does advising count)?

You'd have to ask him to know for sure, but I would expect "full-time teaching faculty" to refer to full-time faculty whose duties include a substantial amount of teaching.  It would exclude adjunct professors and other part-time faculty, and would also exclude faculty who never or rarely teach.  I expect that very few college or university faculty positions literally involve teaching "full-time".


Discussing finances with advisor: Am I being selfish?

What you are getting paid when you are not working for your university should not matter. Taking it to a (albeit artificial and ridiculous) extreme, if a top programmer in industry, with a salary of 100k$/year joins a doctoral program in June, would you consider that his salary from January to May is enough so you can not pay him for a couple of years? In my view (and some jurisdictions too), working for free is very close to slavery, and should be avoided when possible.

So, absolutely, you can go ahead and ask her if she will fund you. Your situation is good in the way that if she says no you will have a backup.

With this said, I can understand if she refuses. If it is a single, non continued project, it is not as efficient to hire a person for one month as for three, and if you are not going to do it, she may use the funds to hire someone else for the full time. If you are going to continue doing your usual work during that month, there is not so much difference between being there one or three months, and your case is stronger.

As an extra, during your fellowship, you will probably learn a bunch of new things, so you are an extra asset for your group. You can also offer to give a few seminars on what you have learned in partial exchange for the funding.


I might not get any PhD offers this year. I would like to apply again , what can I do to maximize chances

You've got a couple of options

See what happens with the current applications.  You may be surprised.
Try to get a job as a researcher at your current university.  If a prof. has worked with you and can vouch for you this will be much easier.
Have really awesome GRE or equivalent scores.
Cast a wider net.   Searching "top 10" on this site gets you 200 results!  You may want to apply to schools outside of the top 10 in your field as this seems to be the cut-off most well-qualified applicants use.


What tricks can I use to add value to my poster?

Trying to avoid basic content organization that is already mentioned by this question.

From the added values point of view, I have seen/would have appreciated:

option to take a print-out with an abstract, arXiv/full paper that the poster is based on
have business cards ready/available to be freely taken (you might have to be creative on how to attach/arrange things around your poster/poster board depending on conference organization)
QR code in the poster with a link to a relevant website (source code, open data, etc). I tend to take pictures of posters that I am interested in. And I like QR codes.
have a note (somewhere visible) that you will be available (and be there!) in the coffee shop of the conference location at a specified time if somebody wishes to discuss the research. Reason: sometimes you are presenting research that attracts a lot of people, so you are always busy talking and presenting. So, not everyone gets a chance to talk to you – and their time near the poster is also limited, so they might not come by around the second time - only to find you busy with another person questioning you on some irrelevant topic.
If you are presenting something for which "you can print a simplified 3-D model", not necessarily up-to-scale - that is always fun.

I do not mention the "freebies" that you can giveaway without creating obstruction since they might attract people to your poster but probably will not add value. However, certainly, have them if you can :) I would not complain. Nobody would complain.


What types of industry positions favor PhD over a masters?

I am currently employed in the biotech industry. Hopefully this is helpful but it may all just be obvious:

Concerning research industry positions, jobs are generally classified as PhD (scientist) or non-PhD (research assistant/associate). For scientists positions, sometimes someone without a PhD will be considered if they have significant experience - e.g. Masters plus 5-8 years, Bachelors plus 10+ years. However, PhDs are generally favored over non-PhDs for outside hires. For research asst/assoc positions, non-PhDs are favored over PhD holders, and many companies have policies that prohibit hiring PhDs.

Concerning non-research industry positions, holding a PhD will give you an edge over BS/MS holders, but you have to compete with other specialized degrees. For business developement and upper management positions, you'd have to compete with MBA holders (along with internal hires from research/scientific management). For legal positions, you'd compete with JDs and certified patent agents. For project management, there are certifications as well.

If you were to hold MBA/JD/additional certification AND a PhD, you would be extremely marketable for these types of positions. It's a lot of work to add something like that on after finishing a PhD program, but companies often love to have PhDs on staff in those types of positions - but generally you need to have the other qualifications as well.

Edit: Also, the best people to talk to are professors from your current/old department who are on any company's board of directors. They will know exactly what kind of people a company wants to hire, and will be able to tell you how to target your job search, or what kind of experience/credentials matter most.


Visa application for PhD studies Australia

All state schools in Australia are free. Just enrol your kid in one that’s close to your house so that it’s convenient to drop them off.
Australian schools fall into one of three categories: state schools run by the state government, which are free (though they might charge a small enrolment fee), independent schools which might or might not charge their students for tuition, and Catholic schools which also may or may not charge tuition fees.


How should I deal with a professor whose weak language proficiency is disturbing our paper's writing quality?

As a French native speaker whose English was gradually improved over the years, I've been on both sides of this kind of situation, and there are different aspects to consider:

If your collaborator does not like you fixing typos, then there is a real problem;
It is usually accepted that papers are not written in British-English, nor in American-English, but in Global-English, and being a native English speaker yourself might not be strict advantage. If your collaborator has successfully managed to publish dozens of papers, then either his style is somehow accepted, or all his papers have been written by others, in which case he wouldn't mind letting you write the paper in your own style;
The style of an author is personal, and changing it can be seen as touching the ownership of the text, and can also be seen as offensive, especially when the gain of the modification is not immediately perceived (which might be the case for non native speaker, a "better" expression does not necessarily strike as an improvement). This is particularly true if you only change one expression: if you were to rewrite an entire paragraph, to change to some extent the content, it would probably be easier, since you've clearly improved the text.
At least for me, there is a clear notion of trust of people I'm working with. There are some people I completely trust, and I don't care a second if they modify my text, but I would be reluctant to see my text modified by someone I just started working with, especially if it's only for cosmetic purposes, like picking the best expression or word when the original one is understandable/correct, or changing a notation, or reformatting the paper, etc. I'm not saying I would be against, but I would need to understand and agree with the gain. In my opinion, this is mostly a notion of trust rather than seniority.

In summary, let it slide, as long as it does not impact the overall clarity of the paper, especially in the first stages of the paper (some expressions you don't like might disappear naturally after a while, replaced by new content).


Is a Masters Degree mandatory to gain entrance to a PhD in US

No, in a rough manner...

There are a multitude of Ph.D. programs, presented by US universities, within which the M.Sc. degree would not be as a mandatory factor for entrance the target program.

As a matter of fact, direct transition from B.Sc. (first-class or 4-year one) to Ph.D. would be a research plan for the future action within the academia, where one often seeks a M.Sc. degree for the participation within the industry.

All in all, you better check the admission requirements of the target programs, by case, to realize the necessity...


Can two universities have the same name?

There are a number of Belgian universities which were one institution formerly, but have been split in two independent institutions during the language conflicts between the French and Dutch speaking citizens in the 1960ies. At the moment they in principle still carry the same name, but in the different languages. Examples are the Free Universities of Brussels (Vrije Universiteit Brussel and Université Libre de Bruxelles) or the Catholic Universities of Leuven (Katholieke Universiteit Leuven and Université catholique de Louvain).


How can I address my career future with my current PI?

Your advisor has the duty to inform you if you are meeting expectations, and to notify you in a timely manner if your contract will be renewed or not. Politely bringing this up at the end of the meeting should not cause conflict with your advisor—unless your advisor is a control freak (in which case it's not exactly a bad thing that you'll need to move on!).

However, I would have this conversation as soon as possible, as the end of your contract will be here quite soon. You should inform him, if you'd like to continue working with him, that such is the case. You should also politely mention that if the finances aren't secure for a commitment, that you will need to consider additional job opportunities to ensure that you are not "stuck" looking for a job without a current source of income.


How much code in a computer science thesis?

For someone who's already enrolled, this is prime ‘ask your supervisor’ territory, since thesis requirements and expectations vary enormously between countries, universities, departments, and research groups.

If you’re not enrolled yet and want to gauge the code requirements at a particular department before deciding to do a Master’s there, you have a few options:

Many universities have a publicly accessible, online research repository where theses are deposited. Download some recent Master’s theses from your department of interest and see what they do.
If your department of interest is not too hard for you to reach physically, you can go to their library and peruse hard-copies of theses.
Just about every university should have a written handbook for theses, and these are often publicly available for download. You may find some guidance for code inclusion here.
Contact a professor at the department, or an alumnus of the department, to ask your question. It can be hard to get a reply to an out-of-the-blue email to an academic, but if you are seriously considering study there, and make this clear in your enquiry, your chances should improve :).

Visiting the department, looking at past theses, and making contact with professors are of course things you'll want to do anyway if you’re thinking of applying to that department, so checking the amount of code needed in a thesis is really just another item to add to your checklist when you’re finding out about the institution.


How to know if a paper is allowed (by publisher/journal/conference) to be put on arXiv?

Check the publisher's website. They should have policies for putting papers on arXiv.
For example here is Elsevier's policy page, and:

Authors can share their preprint anywhere at any time.
If accepted for publication, we encourage authors to link from the preprint to their formal publication via its Digital Object Identifier (DOI). Millions of researchers have access to the formal publications on ScienceDirect, and so links will help your users to find, access, cite, and use the best available version.
Authors can update their preprints on arXiv or RePEc with their accepted manuscript .

So for this publisher the answer is "yes", you are allowed to put papers on arXiv as well as update them once the peer review process is complete.


Ask professor for reference and at the same time propose to do phd with him? (UK)

Keep the email brief and to the point. If you haven't spoken to him in a while, introduce yourself and tell him what you're doing (1 sentence should suffice).
Explain that you're applying for PhD positions and that you would like him to write a reference for you. It's probably a good idea to mention your research interests and remind him of any projects you worked on together, so he can write an effective reference for you. At this point, you can also ask if he is currently looking to take on a new student, as you're very interested in his research and would like to work with him.
If you do end up applying to work with him, you will need a reference from another academic. There's no point him writing a reference for you which he will then read. He will be able to find out more about you and get the full picture if you have a reference from someone else.
Note that most UK PhDs will require at least 2 references anyway, so you should have at least 3 people in mind who you can ask should the need arise.
Your first email to him may go something like this:

Subject: Reference letter
Dear Professor X,
Hope you are well. I am writing to let you know that I am planning to apply for PhD positions in Y and consequently need some letters of reference. Would you mind writing a reference for me?
It would be helpful if you could mention when you supervised my work on project Z, as this project was very successful and the topic is in line with my current research interests.
On this subject, I noticed that you recently published a paper on topic Z. Are you currently looking to take on a PhD student? If so, I would be interested in applying for the position, as our research interests align well and we had some success with the project I mentioned above.
Many thanks and best wishes,
George Welder


Should I post the data my project was tested on in the paper?

If you can make the data set available to the community in some way, you are doing it a good service, because it will allow other people to use your dataset for comparison and for their own new works.  If they find it useful, it will also help you, as the people who use it will cite your paper as the source.

I would thus say that yes, if you have a good way to either post it online or attach it to your paper as supplementary information, this this is a good thing to do.


Is it of academic value to submit two papers describing two different but somewhat similar architectures?

You can submit both papers to one or two different conferences, as long as you have two new contributions in them.

Side Note

It is advised not to cut the "meaty" part of a very nice contribution, into two or more different papers/journals. This sort of "slicing" put your future academic life at risk, because there are some academics that write many poor papers, by just slicing a contribution into different papers; and they are very well known for their "efforts". So, do not put your academic career at jeopardy, and think this through (i.e., contribution(s) you want to discuss in each paper).


What to do when you do not get an answer after 1 year

I suspect that if you've not heard anything after a year then either they have a HUGE backlog of papers or they have rejected your paper and did not have the decency to tell you. Sorry. I think we've all been there at least once. :-(


(Paper submission) Institution vs affiliation

Institution usually refers to the institution that the work was done at, or at least who pays the bills for that particular author most of the time.  For many authors this is the only institution they are affiliated with, so it really makes no difference.
Affiliation refers to other organizations that the author is affiliated with.  For instance, say I am a researcher at university A, but a medical doctor at an associated hospital (I'm not, but just say...).  Then I might list the university as my institution (because they paid for my lab space, perhaps they had the research ethics board etc) but I am affiliated with the hospital as well, which is where the research subjects came from.  I would list both, because both organizations should be recognized for their financial or in-kind contributions to the work.
Sometimes, authors have multiple affiliations just because they've been given appointments by other organizations, whether because they want to boost their prestige or because there was a relevant reason for this to happen.  For instance, if a university researcher is working on a space mission and they are given appointments by some NASA research centers, they might list those appointments as their affiliations.  These organizations may have contributed lab space, equipment, funding, personnel etc, all under the guidance of the researcher, and the organizations should therefore be listed.
Sometimes it is necessary to divulge a conflict of interest as well.  Say that I am a university researcher doing research on a drug for a company that I am also on the board of directors for.  I should mention that company in my affiliations (among other things)