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Graduate Program - CCNY Language Exam
Got into the Art History program and see that I have to pass a language exam at some point during my studies.
Has anyone here taken the exam? I'd be taking it in Spanish.
I can maintain a conversation and am about a fourth grade reading level. I'm not terribly disciplined so I'm considering taking a non-credit Spanish course this summer to prepare. I know one's mileage may vary, but how difficult is it on the whole?

Ask someone in the department what the real requirements are. It may be that vocabulary will be the stumbling block, but it may also be that reading some book(s) in Spanish about art or artists is the sort of thing that is required. Probably not so that you can ask directions in the subway, I think.

I don't have any personal experience here - but some googling suggests that CCNY only offers a M.A. in art history - and that the language exam it requires is about reading skills rather than conversation:

Each semester City College offers exams in Spanish, French, German, Italian, Classical Greek, Japanese, and Latin. This examination tests your ability to translate a short document from your chosen language into English. You are permitted to bring a dictionary to the exam if you wish. You must register in advance for the exam. Each semester we will post the deadline for registration. You can register for this exam in the MPIR office during office hours. You may prepare for this exam in any way you choose (for example, taking a class). If you are multilingual, you will not need any special preparation.

This seems in line with language requirements in math programs - the idea being that there may be important texts in your field that either a) haven't been translated to English, or b) would be advantageous to read in the original language.


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Is it possible to do a PhD in one field along with a bachelor's degree in another field, all at the same time?
I have an MBBS (Medicine bachelor and bachelor of surgery) degree and I am currently doing my master's in biotechnology and planning to move on to a PhD in the same (or a very closely related) field, Meanwhile I am very eager to study theoretical physics and I was initially planning to get going on it right after the PhD. But, for time purposes, is it possible to do both simultaneously?Is it applicable/ practical?

It's probably possible, but why do you want to that?

Quite probably possible, but it might be better to get a PhD in theoretical biophysics so you can finish faster.  At least in the American system.

Do you intend to make theoretical physics a career? If not, you may be better off getting the PhD as quickly as possible by concentrating on it, and auditing physics classes as a postdoc or professor later. A PhD can absorb all the time you are willing to spend on academic pursuits, so any time you spend on something else will tend to delay it.

The usual disclaimer applies here: the answer depends on your country, your university, your program, etc etc etc. It also depends on you. There are many variables here and not enough of them have been defined, so no one can answer your question definitively.
Let's theoretically bound a few of those variables and do a thought experiment by answering this.
Let's say that for the sake of argument, you are a genius who can not only get done work at an incredible speed, but who can also comprehend and understand all the work in front of you without issue, and this applies just alike to everyone around you who you may have to do any form of teamwork with (thanks O.R.Mapper). Then yes, you can do both of these things at the same time (because the main limitations here are time, comprehension, and energy) - provided you aren't doing them both at a university which has a rule against this kind of thing. As long as you handle scheduling conflicts in a reasonable way, yes. This means: If you have a time where you NEED to be doing obligations for one degree or the other (physics degree = unmissable physics labs even in a theory degree, for example, or exams) and you can make it to all unmissable obligations for both degrees (say they're in the same university or the same area) then yes. However I can imagine quite easily that you will have to resolve scheduling conflicts often. You will probably have more schedule obligations with an undergrad degree than with a postgrad one and it's tough to be excused from those, even if you have a good reason. I'm thinking about things like practicals, scheduled exams, and other things you really can't miss. I'm also mostly thinking about how it was for me in the UK system, and perhaps in other systems scheduling is more flexible, so YMMV.
Unbounding that variable a little: I will state the obvious; a physics degree is difficult. A PhD in biotech is also likely to be extremely difficult. You are a human being. Folks struggle with bachelors degrees, folks struggle with PhDs. I think that any person who is likely to be imperfect (in a totally normal way) is liable to struggle with one of these, not to mention both of them at the same time.
Personally if it was me trying to do both these things at once, I'd be so overloaded and stressed and unable to learn after only a short while that I wouldn't be able to do it. You would have to have impeccable time management, extremely prudent stress management techniques, and you'd never really have a proper 'break' from working or studying because both of these things are full-time+++ jobs. You'd be taking on two of them at once. You'd be subject to the same chances for failure as anyone working two 40-70 hour work weeks. Whether you succeed or fail is a function of how well you handle all of these stresses, and how you allocate the time. And how little you value sleep. I think, but I don't know for sure, that how 'clever' you actually are has less of an effect on your success than the above stuff. You have proven your intellectual capacity already with your qualifications, but a PhD and a BSc at the same time is serious business and even the most clever humans in the world would struggle with it from even a logistical perspective alone. I know that if I tried to even have a part time job during my physics degree, I'd have probably failed. My friends with jobs did fail. I was told by the people coordinating our program that it's this way by design; it's designed to push us to our limits to show us what the research world is like, and to differentiate between good, better, and best.
And this isn't even stating the most obvious part: When you're writing your thesis, you will have time for nothing else.
Since my answer has really been a non-answer I will leave you with this:
I didn't do a theoretical physics degree, just a 'normal' physics degree. I had friends in the theoretical program. They still had to do one academic year of unmissable physics labs for 4 hours every week (to demonstrate the principles of basic physics). They still had to sit exams which were unable to be scheduled to a different day/time. They still had to study with us during 60 hour work weeks to understand the material in the months leading up to exams because there were so many of them and because the material was so vast (this applied even to the insanely clever ones). The only real difference between a theoretical degree and a normal one was that you're able to do theoretical physics from anywhere where you can concentrate (so you can do the 'research' part of your PhD mostly from home if your supervisor doesn't ask you to be in the workgroup's office and if you don't need their help to get things done). This is where my 'depends on program' disclaimer comes in; it might be different where you are. In fact, it almost surely is different.
A lot of it will come down to your motivation level and your ability to multitask without fail. Why do you want to do this (it seems like a strange choice)? I don't ask because I'm being snarky; I'm asking because if you really do do this, this is a question you'll be asking yourself in what I can only suspect will be a very short period of time.
If you want it enough and you're really really really good, sure, go for it. The long and short version: There is no reason why you can't, but there are many reasons why a person would not succeed at this.
Would I recommend it? No way. In the end, you are a human (even if you are really good) and something will have to give way eventually.

I suggest an addition to the initial sentence starting with "Let's say that for the sake of argument": "..., and this applies just alike to everyone around you who you may have to do any form of teamwork with."

great point @O.R.Mapper. editing it now

" Why do you want to do this (it seems like a strange choice)?" Ca y est.  I would suggest moving this question further to the top of your (comprehensive, good) answer.

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Would this work be considered a publishable cs research?
I was able to create a new version of a known algorithm with a reduced space complexity than the original by using a different data structure from the one used in the original. It's something like what Fredman & Tarjan 1984 did for the Dijkstra algorithm's time complexity by using Fibonacci heaps. The only difference is that these guys created Fibonacci heaps, I did not create the data structure I used in my work.
Would my work be considered by a respectable journal?
If no respectable journal would accept it, should I consider self-publishing it to, say, arxiv? or should I forget the whole "publish as research" thing and just write a blog post about it?
P.S: I'm a fresh CS graduate and I'm not affiliated with any post-graduate program, so I don't have an academic advisor to ask that question to.

Do you know if space is an important limiting factor for the typical use case of your algorithm? How about runtime? Is it parallelisable (so suitable to run on GPUs, where a lower memory footprint is great)? I think this are important things regarding applicability.

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Separating academic identity from social identity
I would like to start publishing scientific papers soon. This issue pertains to the name I will use when publishing.
Basically, I would like to keep my personal and academic life separate and my question is "how can I do this?".
To make it clearer why I want to do this, I'll mention that my current legal name is associated with a certain subculture which is quite unconventional. I want people searching/Googling my professional name to only be exposed to my "academic identity", and people searching for my legal name to only be exposed to my "social identity". There is nothing illegal going on. I'll give an example which is close to reality but I'll refrain from giving exact information. The example is that my "social identity" is an author of erotic novels while my "academic identity" writes papers in mathematics. That's not too far from the reality.
I would assume I am not the first one to have unconventional interests outside academia, the issue I guess is that my legal name is already tied to such an interest, which is a problem. And yes, this is quite amusing; feel free to laugh
I would be thankful for any ideas which would allow me to fulfill both my passions, despite their disharmony.
Basically, I don't want the names to mix together when someone searches for one of them, but I still want to be able to prove that I wrote the papers (in case I want to use them when applying for a job or for grad school). Hopefully there is some way to achieve this.
Other creative ideas to solve this issue are always welcome; maybe I am focusing too much on the name thing and there are other solutions.
I'll wrap this up with some ideas that I had:

I could just use a pen name for my academic papers I guess. I have finished my BSc lately. Problem here is that if I later want to apply to grad school, and I want to show that I have published papers, it could be hard to prove that I have written them (will it? maybe I'll have a pen-name on the papers but prove ownership by other means? like the email address on the paper?).
I could use a different spelling of my legal name on the papers (my legal name is not in English anyway, though I graduated from an English speaking university so my BSc has my name in English). That seems like they could still be linked relatively easily though and one could potentially show up when someone Googles the other name.
I could take on a new middle name (e.g. I could use a variation of my late grandfather's name, which I would gladly do) and use that as the first name in published papers (that seems like it could potentially work).

Some more comments

My last name is very common; my first name is very uncommon
I am aware of course that if I go to grad school they'll probably Google my legal name as well, and of course people who know me personally would be aware of what I do. It would be nice to limit it to those scenarios though.
Yes, I know I should have thought of this before linking my legal name to unconventional topics. I did not tell the whole story though and there was a reason for that.

More than one woman I know of has done this.  Publish under her original name (the name she used in her first paper). But when she married, changed her hame to her husband's for social purposes.  And kept the married name even after her divorce.

What's the threat you are most concerned about? My main fear if I were in your position wouldn't be research colleagues connecting the identities, but rather students, particularly less mature students in beginning classes I was teaching. I don't see how to prevent that unless you thoroughly separate the identities (to the extent that your colleagues never call you by your current first name), which is a different matter from which name you use on research papers. There's also the issue that treating this as no big deal may attract less attention than going to great lengths failing to hide it.

This might be relevant to an answer, but how common is the name? If you can easily find tens of people with similar names on Facebook or LinkedIn, then people might just dismiss things as a coincidence.

In case you didn't know, if you write a Ph.D. dissertation and your legal name is on it (which might be a requirement), then it might show up at ProQuest (a web site I use quite often to verify identities and to obtain complete names). Also, if you obtain a Ph.D. in mathematics, then your legal name will likely show up at the Mathematics Genealogy Project web pages. I don't know which other fields have web pages like this, but you should anticipate all fields eventually having something similar.

If you are worried about showing that it was you that wrote a specific paper, you can write to the journal editor and ask them to write a letter stating that they know your legal name. This requires you to disclose your real name to the editor, but if you make it clear that you expect them to treat it as confidential information then it would be a huge breach of editorial ethics for them to disclose it.

Closely related: If I publish under a pseudonym, can I still take credit for my work?

One possible issue you may encounter: the institution that employs you will need your real name, and in some places, you are assigned a non negotiable email address name.surname@institution.edu, even if it turns out ridiculously long (I do know one case that had to fight for a couple of weeks to shorten it because it was very long and difficult).

@AnonymousMathematician I guess if I use a different name in papers, then at least there is the potential of hiding it later if I end up even having students. It is very possible, if I later go to grad school, that I end up going into industry and do not become a lecturer. My main concern is still that people looking up the name which appears in papers get results related to the "unconventional topic" or vice versa.

Also be aware of the predicament you can end up in if a student (who really needs an A) discovers your secret identity.

@rjzii my full name is very rare, because my first name is rare. My last name is very common. There are maybe like 2-3 people with my full name which show up on Google, but the ones who aren't me show up much lower in search results because they don't have much of an internet presence

Very few of their readers know much about the personal lives fo Schrödinger or Keynes (and even fewer care much), to put two better known examples from among the many, many available examples. Those in your subculture won't care that you also publish scientific papers, and scientists in general will just block out what appears to be irrelevant.

Here are a few considerations:
Using a common name in place of a unique name will look unusual, since people who choose to publish under a variant of their name typically go in the other direction, to make it easier to identify their papers.  Everyone who learns about this will assume you either made an unwise decision about which variant to use, are trying to avoid prejudice based on your name, or are trying to disguise your identity.  In any case this change may attract attention, which is the opposite of what you want.
To separate your identities, you need to use your professional name in all professional contexts.  I.e., your university web page should use it, your colleagues should call you by this name, you should use it when you give talks or attend conferences, etc.  To have a successful academic career involving research you need to develop a scholarly reputation, and that can't happen unless everyone connects you with your publications.  That means either they connect the two identities or they know you under the name from your publications.  (In particular, it's not enough for you to be able to prove that you are the author.  In order for you to have a successful career, in the long run everyone must already know you are the author.  This is not such a big issue for graduate school applications, but it's a major factor in getting tenure.)
I wouldn't worry too much about proof of authorship.  This is not so easy to determine from the name anyway: even if you published your under full legal name, how would anyone know you weren't claiming papers that were written by someone else with the same name?  One big clue is your letters of recommendation.  If the letter writers discuss your papers, then everything will be fine.  (While if they don't discuss your papers, then that's a problem regardless of the authorship issue.)  At that point all you need to do is include a sentence in your publication list saying "My publications are under the name X."  You don't need to explain why, just to clarify the facts so nobody is confused.
Once you have started publishing, substantially changing the name you publish under is highly disruptive.  It can be done if necessary, but it may hurt your career by fragmenting your reputation, and the only way to combat this is by loudly and publicly connecting the two names.  This means you should try your best now to choose a variant of your name that you would be happy using for the rest of your career.
It's worth thinking about whether you need to do this.  In my experience, academia is tolerant of eccentricity and impressed by confidence.  If you treat this situation like it's no big deal, then I'd guess that most people will ignore it and anyone who tries to gossip about it will risk looking provincial or small-minded.  However, this of course could depend on the details of your situation.  (And there's also the issue of students: first-year university students are on average quite a bit less mature than faculty.)

I would accept this solely on the ground that it's written by Anonymous Mathematician who would be an expert in this sort of thing.

It seems more challenging to conceal your legal name from students than from readers of your publications - I guess most universities would list you by your legal name in course announcements.

Depending on your local laws, it may be possible to be employed as, and enrolled as under an "common use name". I am fairly confidant that is the case where I am, because Australia doesn't have a strong notion of a legal name -- a name becomes yours when you use it enough.

Thank you. I am not sure where in the world you are from, but I did see @Oxinabox mentioned they are in Australia. I am likely to pursue my postgraduate education in Australia. Would you know if in Australia, as well, I would not have a problem proving authorship of the paper if it was written under a pseudonym?

I would not know. But I doubt it would be any kind of problem, if you use a name consistently in Australia it becomes your legal name.  Beyond that I suggest reading http://academia.stackexchange.com/questions/8603/ and if that does not answer your questions make a new post. (I see you deleted your old comment and then reposted it to "ping" me.)

More of a comment but too long.
I don't get it.
If it's okay to use the legal name among your colleagues:

they'll probably Google my legal name as well, and of course people
  who know me personally would be aware of what I do. It would be nice
  to limit it to those scenarios though.

then why do you care if the readers, who are people so distant away, from next school to five continents apart, know what your another passion is? Didn't you just rank the contact rates and degree of importance in the wrong order?
If I read a paper and tried to Google the author to know more, and then I found out a person with the same name does some very eccentric thing, to be honest I'd probably just dispel that as a coincidence or "ha, interesting" and then move on. Researchers just don't do research and nothing else. To me you will just be an author whose article interests me, whether you do other gigs or not does not affect how I see your paper, unless your other gigs were about how to fabricate data or something along that line.
If you do feel so strong about this, I would suggest changing your legal name instead. Keep your former legal as your passion-related name, and use the new name in all other settings including jobs and publications, etc.

To be honest, independently on how uncommon that name is, I'd probably assume that the "erotic novel writer" its just another person with the same name. Thinking that people in academia has lives outside it is something my brain would probably never process!

@AnderBiguri There are pictures of OP on the internet probably.

Generally speaking, it is possible to use a "pen name" for academic writing, or really for your entire academic career. I think using a different last name would be considered somewhat strange, but assuming your last name is common enough not to be an issue ("Smith") you could easily just use "Karl Bob Smith" rather than "Avdo Rian Smith" for all your academic affairs (except official statements) without raising too many eyebrows. This should largely alleviate your immediate problems, as long as your "unconventional topics" are not also linked to your face (if it is - think porn starlet - your problems are bigger; in this case I would suggest dropping all hopes of keeping it a secret for any amount of time and being super upfront with your past / side project).
However, be prepared that it's likely going to be a leaky secret anyway. Using a vastly different first name will divert the casual name googler and your random conference acquaintance, but I would assume your cohort in grad school is going to find out at some point. There just are places where you pretty much need to use your legal name, such as some forms. And once a few persons know, the message is going to spread with a speed proportional to how raunchy your secret is. Another problem is going to be that the places where you maybe would really want to keep things secret, such as grad school or job applications, are also the ones where you sooner or later really need to use your legal name. In that sense I am wondering how much you will actually win by using an academic pen name.

I don't think changing your last name would be considered particularly strange actually, I know a number of women who continue to use their maiden name for publications even after having having changed their official name when they got married. I also know a man who changed his surname mid-career too.
Something to bear in mind is that university email addresses (at least once you are faculty) are often of a form that include your full name, and they may be harder to change.

Thank you for the answer! Fortunately, it is only my name. If I go with using a different first name, would you expect there to be problems proving that I have published those papers when I apply for grad school? could you suggest how I could prove it? would having ownership of the e-mail address which appear in the paper suffice?

@avdorian Somebody in the US would be more qualified to answer this, but I would not assume that you need to prove this if you say that Karl Bob is your academic pen name.

@xLeitix I went through the US academic system (though I'm not there at the moment, if that means anything) and as far as I've ever known, proving you are the author of a paper generally does not involve any comparison to your legal name. Actually I'm not sure how one would prove authorship to an admissions committee, because I've never heard of it being required.

Thank you for the help. Can I also ask why it is that changing a last name is considered more strange than changing a first name? and are there unique problems that arise due to changing the last name which do not arise when one changes the first name?

I'll also mention that there is a good chance I'll pursue postgraduate education in Australia. Would anyone know if in Australia, as well, I would not have a problem proving authorship of the paper if it was written under a pseudonym?

Do you have a middle name? There are precedents for initializing away your first name. May look a bit pretentious, but not that terrible.
So if your real name is Avdo Rian Smith, and your unconventional community knows you as Avdo Smith, start going by A. Rian Smith in your papers. It is not a complete change, so it will cause less people to go look you up than if you had started to publish as Jebediah Smith.
Similarly, if you have another type of name which is not a middle name, you can take it up even if the convention in your country makes it weird. AFAIK, a Spanish man Urbano Ventura Melendez would consider "Urbano Melendez" the proper name to put on a scientific paper - you could use "Urbano Ventura" instead, even though it goes against tradition. A patronym from some Slavic countries would work too, if it is not reserved for other purposes like a Russian patronym.
In the end, if you only have a first name and only a surname in your passport, invent a middle name and you can still use the initialized version. If your first name is Avdo and the last one Rian, write A. John Rian on the paper and tell your coauthors you are really Avdo John Rian. If they know about your hobby, they will probably understand. If they don't, you could make up some story, or tell them the truth. Or just refuse an explanation - they will think you pompous and excentric, but you may feel better with that than either risking being exposed as a liar, or having your coauthors know your true hobby.
If you go the "middle name" way, you may want to start introducing you by middle name - surname at conferences too, so the community will get to know you under that name. If somebody overhears a close colleague calling you by your first name and asks why, the explanation that one of them is the first name and the other your middle name will be enough.
And in the end, having your hobby known may not be all that problematic, depending on the discipline you publish and the exact nature of the hobby. Scientists tend to be broad minded people socially, and especially the less traditional disciplines can easily accept something which a young person might be afraid to share with professional contacts. You might want to ask people who know you, are outside of your community, if they would advise you to try to hide your hobby. Also note that as a scientist, other scientists are more likely to search for your name in specialized databases like Pubmed or DBLP than just type it into Google.

A small correction: in Spain, if one had to choose one surname, it would usually be the first, unless it is very common and the second is not. Another common thing is to merge them with a hyphen.

Thank you for the advice; it sounds like a good idea. One thing I am not sure about this however: when one submits a paper to a journal, do they have control of how their name is initialized? I understand I could do it in the paper itself, but what about online databases? would they not just initialize the middle name? i.e. I imagine that they would ask me to put in my first name, middle name, and last name, and then if I type "Avdo", "Rian", and "Smith" repsectively, they would abbreviate it as "Avdo R. Smith".

Database curators don't contact your university HR to ask about your legal name. They take the paper and copy whatever is on the paper into their database. And you write on the paper whatever you say your name is, so "A. Rian Smith" should be OK. Submission management systems (like Easy Chair for conferences or whatever homegrown stuff the journals use) can be trickier. If in doubt, type in "A. Rian" in the field which says "first name". If a coauthor of yours is entering, make sure you're around to make him enter the name you wish and not what the name he knows you by.

How much effort you put in differentiating your social identity to your academic identity they will still be connected by the people around you. I think you could just accept the reality and embrace your weakness and make it your strenght.


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My co-authors want to remove my name from manuscript because I am "not in science anymore," how to correct this?
Two years back, was working as an research associate then have to leave the lab due to some family issues. My work was significant enough to be included in the manuscript and I was told that my experimental results will be a part of the manuscript and I will be coauthor in the paper.
Time has passed, the paper was rejected, revised and submitted. Now, the paper is again in communication, and I am being told, that as I am not in science anymore, my name is being dropped from the paper. I am trying to contact them but they are not responding. I am very much in science, but have taken a break. What should I do, if my name is removed from the paper?

I added a close flag because I don't think any of us can give generalizable advice in this particular case. My only suggestion would be that you contact the journal editor cc: the lead author and try to work this out. In the worst case, you would bring this up with the Office of Research Ethics at the lead author's institution. But both are drastic measures and apt to lead you to burn bridges.

"not in science anymore" is no reason not to be included as an author. The only question to ask is whether you made a meaningful intellectual contribution.

@RoboKaren Indeed drastic measures, but for a young researcher's CV even a single publication can be very important (i.e. high payoff if it works). Also, one can argue that an collaborators that do not respond mails in important issues is an already burned bridge.

A bit less drastic than contacting the journal editor would be to contact the head of the department in which you were working. You could explain that you need to discuss authorship on the paper but are having trouble contacting the other authors.

I would go so far as to say there's no such thing as "being in science". If my postman suddenly solves P vs. NP tomorrow, nobody is going to care what his day job is. The value of the contribution counts. Science is not some club you're only allowed in if you work for a university. Your lack of an affiliation is an administrative glitch. You made a contribution, and if they publish without acknowledging it, that's a serious breach of ethics.

@Peter Well, they'll care, but that's mainly because they'll start writing the guy's biography immediately, and we'll know what he ate for breakfast on May 3rd, 1996 in no time...

@Peter: I was thinking of Dilbert's garbageman when I read your comment.

Authorship wars are common and they suck. I suggest you discuss your plans to reach out to the journal editor with the primary PI, maybe they can change their mind. I don't know what being in science or not has anything to do with your contribution being ignored but I would understand an argument that suggests a ton of work has been done since you left to bring the paper to publication.

This smacks of gender discrimination.  Women more often take a break from academic work and studies for family reasons than men.
It might be helpful to contact your university's Office of Equal Opportunity.
You might be able to file a complaint with your state's Division of Human Rights if appropriate in the specific case (which wouldn't cost you anything, by the way).

The colleagues' behaviour is scandalous, but the OP makes not the slightest hint in their post to indicate it's about gender. The whole argument would be equally valid if it was a man taking a break or paternity leave. Let's keep the issue focused on what it is: misappropriation of scientific credit.

@CaptainEmacs - to notice possible gender discrimination, one has to look a little more carefully.  Those who perpetrate it rarely make a fanfare announcing "I am practicing gender discrimination!"  Reassurance for Captain E: you may rest assured, formal complaints are investigated extremely carefully.

I am not saying it isn't. Having had a female friend being victim of gender discrimination, as well as mentored a student who had a history of being gender-discriminated against in the most blatant fashion (at a time when it was still fashionable for people to do that and shrug off any complaint), I have a deep revulsion against any form of discrimination, for whatever reason. However, I do believe that pulling in the accusation of gender (or other) discrimination without very strong evidence (not just a "smacking" of it) or using it as a tool does the (just) cause a disservice.

@CaptainEmacs - You and I aren't in a position to investigate or judge -- firstly, because we don't know the whole situation.  But I can suggest the OP consider a possible course of action, if it is appropriate in the specific case.  Often, the experience of discrimination, through its pervasiveness and subtlety, dulls the person's awareness of it.

I agree with if appropriate in the specific case. If you add that to your answer, I will support it.

It seems awfully sexist to assume the gender of a person without asking first (kidding). But I agree with @CaptainEmacs here. Claiming gender discrimination in every situation involving a female does nothing to bring about gender equality. Having said that, you could be right, aparente001. This very well could be a situation of gender discrimination, but I agree that your question needs editing. Or it might be more appropriate to ask the OP if this is possibly a factor, and if so, it could be included in the question. This would certainly be relevant information.

@haff - I suppose lisa might be a man -- but traditionally it's a woman's name.

If you can't resolve this issue with the editor of the journal (or you don't know the journal), the PI isn't responding you could also go the university/agency/company/organization and discuss violation of an ethical code.

You should write up your own paper on the subject where you cite the paper in question but also mention in a footnote that they failed to properly acknowledge the source of some of their results. If the results are of sufficient interest, the paper will likely be accepted for publication. A paper with your results authored by you is what ultimately matters.

Any sane editor would not allow an author to make an accusation like this in a footnote to a paper.

It depends, if the paper is of sufficient interest and the dispute it mentions is within that context relevant, then the paper may well be published.

The paper you link to is not the same thing at all. The authors of that paper complain about another group ignoring their work, which is a far cry from an accusation of academic theft (which is what you are proposing). Can you find an instance of an author making an accusation of academic theft in a footnote of a paper?

If it is indeed academic theft, there are much better forums to prove it than  the editorial room. Also, exposing this argument to the public this way most probably hurts much more the weaker side, i.e. OP.

My suggestion is not to tackle the "academic theft" aspect issue head on, rather to sideline it by getting your own results published under your own name and mentioning the previous published result as flawed w.r.t. sourcing/authorship (the reason why you mention it is because you need to cite previous work). This will make the "weaker side" come out a lot stronger, because the focus is on the academic work rather than on moaning about being treated bad.

I left out the "academic theft" issue, if the OP ignores this herself let other judge how it should be called, then she'll be fine.

@Count Ibis: As a referee, I delayed publication of a paper for around a year until I got the authors to remove a sentence with a similar accusation (the year was the time it took for the authors to send in a manuscript without the accusation; they first tried to tone it down). Such accusations have no place in a scientific paper, especially if there is no proof available one way or the other. This is not a good idea.

I'm taking the OP's comment "Now, the paper is again in communication, and I am being told, that as I am not in science anymore, my name is being dropped from the paper." at face value here. If the other authors can remove her from the author list, then why can't she do the same to the other authors? Of course, we can speculate that what the OP writes may not be correct or that it's not the whole truth. But here we can only address questions by assuming that what the OP writes is a correct reflection of the situation.


text:
Is there a code of ethics for Ph.D. supervisors?
I'm a Ph.D. student in Germany, I got my M.Sc. degree in Finland, I have friends in different countries doing their Ph.D.s, especially in the US, and there are also my fellow students in our group. So I have had the chance to learn about people's experience with their Ph.D. And there's one thing I see frequently which is annoying and frustrating: Ph.D. supervisors (people on tenure track/group leaders/senior researchers/...) are apparently not trained for this job and the job happens to be a very difficult one.
It seems that it's quite common to hear terms like arrogance, micro-management, exploitation of students' capacity, lack of respect, etc. attributed to a supervisor. I'm personally living with it, but I would like to be able to formulate all these thoughts in a meaningful and mature way. I need to have a clear understanding of what I'm going through.
Now I have one specific question (but I'd also appreciate knowing other ways of approaching it): is there a worked and published text on the supervisor-student relationship? like a code of ethics? I don't really know what to name it.

"Ph.D. supervisors (people on tenure track/group leaders/senior researchers/...) are apparently not trained for this job and the job happens to be a very difficult one." Yes!  "It seems that it's quite common to hear terms like arrogance, micro-management, exploitation of students' capacity, lack of respect, etc. attributed to a supervisor. " On the face of it, most of these things are human shortcomings of the sort that training would not necessarily eliminate.  " Is there a worked and published text on the supervisor-student relationship? Like a code of ethics?" None known to me.

Yes, fun facts: professors are frequently trained to do none of the following things critical and necessary to their jobs: teach, supervise, work on committees.  Many won't even be trained in writing grant proposals, another standard facet of their employment.  Some will have a modicum of teaching experience in their graduate years, but this is not guaranteed, and may not be as the lecturer, and remains as sink-or-swim, figure-it-out-as-you-go-because-no-training-for-you either way.

No, we professors are not trained and rarely even mentored; we all just make everything up as we go along.  Yes, it's a hard job, and not all of us do it very well. Yes, some of us (as we are, after all, human beings) are incompetent jerks.  If there's a written code of ethics, nobody has every shown it to me; we make that up as we go, just like everything else.

There is nothing commonly accepted. And you are right that nobody receives formal training in how to supervise a Ph.D. Academia is really still very much in a medieval mode here, where you learn from your master (your own supervisor), potentially work under other masters (changing labs) and then are deemed worthy to have apprentices of your own, who you will treat roughly as your master treated you.
However, if you Google for "Betreuungsvertrag Promotion" or "Doktoranden-Betreuungsvertrag", you will find quite a few templates for formal agreements the supervisor needs to sign in some German universities. The key word being "needs to" - this is compulsory for the supervisors.
Unfortunately, these agreements only cover things like regular meetings between the candidate and the supervisor, and that the supervisor will give good advice and in general ensure that the Ph.D. can be attained within n years. This is all very nice, and any decent human being should already be doing all that is in there, but it's all rather vague. In addition, I seriously doubt that anything like this would be taken seriously in a potential lawsuit.
Bottom line: the good supervisors already do everything that's in these agreements, and the bad ones won't start once they have signed this.

I found something in the U.S.: the AAUP (American Association of University Professors) has a code of ethics.  I couldn't find the most recent version, but here is the original text from 1966: http://www.aaup.org/report/statement-professional-ethics

In agreement with the other posts there is no set code of ethics between universities for a PhD supervisor. Although my university does have a code of practise that I am unfortunately not privy too, although reading university's is. What I do know is that new researchers are required to take in-house training to help improve their teaching abilities. This is starting to become common practise at Uk based universities, due to pressure from the teaching union. And clearly has been beneficial to some members of staff and students. However this only applies to new members of staff with no previous experience.
At my own university they track the number of supervisory meetings, and the content of those meetings. Along with reviews of the the student, conducted by lecturers who are not associated with our lab group, once a year to make sure they are getting appropriate support, and making acceptable progress. Failing these expectations creates problems for the supervisors and their contract renewals, and may even lead to disciplinary action.
Just one personal point, ignore if you like. Personally I believe the issue of poor supervision is down to the personalities of academics and their students. Expectations play a significant role in this. In my own experience my supervisor has been excellent, but the same things that make him excellent me are things one of his other PhD researchers does not like. I'm not sure how much training would help this.

How does your university have a code of practice that you know about but don't know the contents of?  That seems very strange.

"they track the number of supervisory meetings, and the content of those meetings" - because more meetings = better supervision; the closer the content to the original plan = the better the progress; etc.? It can work, though I'm skeptical of this kind of approach, given that the requirement to provide reports on some progress can easily lead to doing the actual research and supervision on the one hand, and a "parallel world" of of semi-fictitious reports that match the requirements on the other hand. Reports to funding agencies based on research grants are a good example of this ...

... phenomenon, which I think is based on the fact that research is by definition supposed to bring up new contents, so any kind of reporting will either be non-standardized (at which point it becomes equally prone the issues mentioned by the OP about current supervision), or abstracted to a degree at which it is not useful any more ("Have N full papers and M short papers been written?"; "Are there at least two concrete ideas for future research based on the current progress?"; "How many core aspects of the grant were discussed in the last status presentation?").

@Jakebeal I know a code or rather recommended practice exists, my supervisor has a copy. I just can't find it on the university website, probably because they store staff documents on the staff side of the university intranet.

@O.R.Mapper I agree, I find tracking and reporting my meetings to be annoying and I often forget to do it until I absolutely have to. It is likely that I have not been accurate given how late some of these reports were. I don't think it helps research either, meetings do but not reporting them, although it does help to highlight poor supervision or the lack of it.


text:
In the United States, how customary is it for professors to not check their emails around Christmas?
I hope I don't sound like I'm complaining, and I understand professors and academics are humans. My question is more of one of inquiry rather than venting. I have e-mailed a few professors for certain professional opportunities. This is not my first time doing so, and I am familiar with proper e-mail etiquette and how to write a message to minimize the chances of a glaring ignore. I have also received replies in the past. However, I have e-mailed a few professors about a week ago, and my inbox is crickets so far. On average, is it customary for academics to take a break from e-mailing during the Holiday break?

P(reply|person) > P(reply|professor) > P(reply|professor,christmas)

You may also find other times when professors ignore work in favor of personal lives: such as other academic vacations (spring break, summer, etc.)  And some may intentionally never read professional e-mails on weekends.  This is some professors; others may be available practically 24/7 and reply within minutes.

If the university itself is officially on vacation, I'd assume all the academics are too and just consider any reply you receive over this period to be a bonus.

This doesn't just apply to academics. In commerce and industry you find this too.

You're basically asking us "a professor didn't reply to me, is it because of Christmas?". How should we know? We don't know you, we don't know the professor, we don't know if they celebrate Christmas or not. It's a pointless question, the only possible answer is "maybe".

I'm one of those critters on a twelve-month teaching contract. That leaves me three times it's possible to take more than a day or two of vacation without screwing my coworkers and students: between graduation and start of summer term, between end of summer term and start of fall... and winter holidays. Do I answer my email over winter hols? I surely don't. This question smacks of "I know you're human, but you're not supposed to ACT that way."

I would find out, for each professor, when their classes start back up. I'd give them until the middle of the first week of the academic calendar starting back up, and send them a polite follow-up email. It's easy for stuff to fall through the cracks during this vacation period.

Yes, it's common. Many take a break from work entirely during this season. Some reduce their working hours to spend time with family, and only answer urgent email. Some may be traveling and have limited or no access to email. Some (like me) may be swamped with grading and other end-of-semester duties and are focusing on those at the moment.
If you haven't heard back by mid-January, try a polite follow-up then.

There is the risk that if the initial email was seen as spam ("professional opportunity "), the second followup could be seen as badgering. There is, however, little that the OP has to lose at this point.

Leaving aside the timing of your request, if you were not my student and cold emailed me about a "professional opportunity," I would view it as academic spam and would put it in the lowest priority queue, right after re-upping my free professional journal subscriptions.
It might just be your phrasing, but from my perspective as faculty, it sounds more like opportunity cost than opportunity.

Inded, I know very few people who answer at all cold calls in academia.

In addition to the excellent answers given already, you should also consider that even those professors that do answer emails during the holidays will usually do so based on perceived priority - and I doubt that your cold-call "professional opportunity" email is important enough to many professors to answer between visits to relatives and stuffing them with whatever their traditional holiday food is.
You should try resending again when the holiday period is over.

While we can't guess for the particular professors you're dealing with (and some professors never really take any time off), it's quite common for people in the United States to take significant time off around the holidays.  The more responsible ones will set a vacation message letting you know when they'll be back, but really, you shouldn't really expect to hear anything from anyone until significantly after New Years.

(I've never set vacation message because it often creates issues with mailing lists.)

@FranckDernoncourt: Yeah plus it's semantically offensive. If you're not going to send a response, don't send a response!!! A response saying "Don't expect a response" is just silly.

@LightnessRacesinOrbit Personally, I've found it quite useful to know what dates my colleagues expect to be away, and highly appreciate a vacation message that includes that information.

@jakebeal: Your colleagues by definition work for the same institution and therefore have the same holiday dates. For personal leave, it may be useful to know. But again you should really know already! Do you not talk to your colleagues?

@LightnessRacesinOrbit Your colleagues by definition work for the same institution and you should really know already.  These statements are simply not true: 1) as with many researchers, I interact with a large number of other researchers at a wide variety of organizations spread all around the world, and 2) many professors take significantly less vacation time than the time between semesters.

should I expect that they will come back to work after Jan 2?

@Ooker Many will come back to work on the first workday after the New Year (Jan 4th this year); some, however, will have taken longer vacations, often all the way until the first week of classes.

@LightnessRacesinOrbit: I can see nothing "semantically offensive" in a vacation message. If you're not going to respond to my message, the least you could do is tell me exactly that. Otherwise, I might be waiting in vain and possibly delaying other processes. In my opinion, not responding at all is almost always extremely rude. That is equally true in the case that usually applies to vacation messages, which is of course not that there isn't going to be a response, but that there isn't going to be a reponse right now, or until .

@O.R.Mapper: That's interesting because I read a lot on Academia.SE about how professors fail to reply to uninteresting emails as a matter of course, and that this is to be considered normal! I would tend to agree in "normal life" that it could seem "extremely rude", but domain norms seem to prevail instead. Perhaps that's all this is too.

@LightnessRacesinOrbit: "Uninteresting e-mails", yes - given that spam and certain forms of cold calls are in themselves rude to start with, I think it is ok not to reply to them, also to heed the don't-feed-the-trolls advice. However, vacation messages are usually unspecifically set for an entire account, where it might be more worth to spend a minute to set a vacation message for the handful of not too uninteresting messages that do deserve an answer.

@O.R.Mapper: Perhaps it's worthwhile on balance.

@FranckDernoncourt fwiw, a lot of systems now support having one message for internal correspondents ("go talk to Sue if you need the lab keys") and one for external ones. I tend to set internal but not external, which neatly avoids mailing list problems!

It's easy for stuff to fall through the cracks during the Christmas-->New Years vacation time, at least in countries for which this is the central winter holiday period. Don't take it personally.
I would find out, for each professor, the academic calendar where they work (this is always easy to find online). I'd wait until the middle of the first  scheduled week of classes, and send them a polite follow-up email. If they don't respond within a week, then they are probably not interested.

First, you are not entitled to the professors' time in matters of your personal professional development. You asking for a favour from them here, and, even if you frame it as a matter of etiquette, it is something you want from them and thus, you should consider yourself more on the side of the obligation then them.
Second, concerning permanent reachability per email: I do not expect my research fellows, PhDs, MSc or BSc project students to respond to emails etc. during weekends or vacation; my arrangement with them is done in advance in such a way that contact during their rest/break time becomes necessary only in the rarest emergency; in which case I escalate to phone contact.
You may want to consider the possibility that the professors you are contacting may want to enjoy the same privilege. Clearly, as your search for a  professional opportunity, this was not unexpected and thus in no state of  extreme urgency, but could have been planned ahead of time by you to avoid the holiday period.
To come back to my illustration, the test is that if you feel it may be intrusive to ring the professor up at 23:00 on Saturday night or during the morning of Boxing Day (which you likely will), you should also not expect an email from them during this time (at least I hope it for the sake of their family).
That being said, some people do not respond during their absence, but then empty their mailbox after they are back to work; I would consider this equally disrespectful on the flip-side of your problem. For such people (or simply forgetful ones), a polite reminder, shortly after the vacation ends, is perfectly in place.

I would think that as professionals, most check their emails several times a day. That, of course, is not the same as responding.

Even we professionals take genuine vacation on occasion.  For example, this December, I spent some time in a place where I didn't even have cell phone service, let alone email.


text:
Arxiv puts submissions on hold for months, ignores email
What is the new fashion of arxiv.org to silently put a submission on hold for many months?
When I wrote to moderation email, the question was ignored.

Possible duplicate of: http://academia.stackexchange.com/q/14511/22733

Since lots of other people are getting their work published on arXiv right now, and other answers show that arXiv is generally quite fast at handling holds and responding, it is unlikely to be a general policy.  That leaves one of two basic possibilities:

You have fallen through the electronic cracks: some database fault or the like knocked your submission off of the moderators' queues and your email is going into their spam filters, so they have no idea that your submission is on hold.
Something about you and/or your submission is causing your submission to be continually deferred while the moderators take care of other business.

It certainly could be #1, in which case I would advise sending another email from another account, politely inquiring as to when you are likely to hear whether your submission is accepted or rejected.
Regarding #2: having no idea about your submission, I cannot speculate on whether it is the problem, but I suppose that it is possible that you have submitted something extremely borderline: hard for them to decide how to categorize and also unclear whether to reject.
If it was just about your submission, however, you probably would have received some response to your email.  If, on the other hand, you are being rude to the moderators, then it's possible you are not getting a response to your email for that reason.  Even in this case, it is unlikely to be an intentional decision (if that were the case, they would probably just reject you) and more likely a case of people just deferring the problem case to the bottom of their triage list.
The recommendation of how to proceed, however, is essentially the same as #1: send another polite email inquiring about when you are likely to hear whether your submission is accepted or rejected.  If you don't hear back in a few days, ask a colleague to send email on your behalf instead.

Based on your comments, I understand that you have put several papers on arXiv. Usually, technical reports or drafts above-the-average get accepted. This one being turned down might have something to do with your new fashion of below-the-average writing.
Not every submission to arXiv is guaranteed to be accepted. Maybe you should revise your work and submit again.

unhelpful; it was not rejected but put on hold


text:
Change in "under review" date
I submitted a research paper to a journal on 30th July 2015 and its status went 'under review' on 19th August 2015. I did not receive any communication from the journal, so I sent a gentle reminder on 11th Dec. 2015. Unfortunately I did not receive any response again. I then waited until 29th Jan 2016 and sent a reminder email again. Fortunately, the editor replied with "Your paper has been partially reviewed and we are waiting for remaining reviewers' response." The editor assured me that they will encourage the reviewer to submit the response.
Now, the status of the paper has changed from "Under review, date 19th Aug. 2015" to "Under review, date 2nd Feb. 2016".
I do not know what should I comprehend from this change in date?

"2nd Feb 2016"?

When the status remains the same, but the status date changes, this often indicates that some of the reviewer comments have been added to the database and the editor has started accessing the database to view the comments. This also corroborates with what the editor has mentioned in his email to you. Probably, one of the reviewers has submitted the review while the others have not yet done so. Once all the reviews come in, the status will change to "required reviews completed."

My guess is that the reviewer they were waiting for has withdrawn or been dropped and a different reviewer been assigned.  There are other internal actions that might cause the same sort of visible change as well, but all of them likely signify progress toward receiving your response.

Thanks for your answer. Might be another silly question, can I expect final decision soon? I mean since the new reviewer has taken the manuscript which is declined/not-responded by other reviewer so he will make review faster.

@user3563929 Unfortunately, there's no way to tell whether the editor will be any more effective in picking a new reviewer this time than last time.  I expect it's likely going to be quite bimodal: either you'll get a decision within a month or else you're going back into indefinite limbo again.

I have experienced such situations as an author, reviewer, and editor. Generally, the reason for such change is that due to delay in reviewer's response or unable to provide review on the paper due to lack of sufficient knowledge in that area. In such case, editor assign a new reviewer in order to review the paper. Normally, each paper must be reviewed by at least 2 independent reviewers, and some editors (like me) prefer 3 reviews so that it becomes easy to take appropriate decision in case any two reviews contradict. Also, if the editor already have received a review or two, he/she asks assigned reviewer to provide review strictly within the review period defined by the journal. I hope you will get the reviews of your paper within the review time of the journal (after Feb. 2'16).

Thanks for your answer. As a reviewer how long would you give to the reviewer to review it ? Also assuming that only one reviewer has given response as 'rejected', would (you as) editor again send it to review to another reviewer or directly reject it ? I just want to guess reviewer's response if only one has responded so far. Thanks in advance.

I'll give a full consideration to the paper while sending to other reviewer, even if one has rejected. However, I will strict to the time specified by the journal to review the paper. I think you know the fact that due to their busy schedule many reviewers send their reviews late.

Today I checked the status and it has changed the date once again i.e. 15 Feb. 2016 under review. Does it mean the reviewer has once again changed ?


text:
Applying for more than one faculty position in a department
I am coming to the job market this coming fall and a university that I am very interested in has a number of faculty positions that were posted simultaneously. Consequently, they are all positions that would be appropriate for me to apply to given my research.
Now, my question is-

is it a faux pas to apply to more than one position in a department?
Is this especially so with a competitive/elite university (e.g. Duke, MIT, University of Chicago, Standford, Carnegie Mellon, etc).
Do elite universities care more about exact fit or research productivity?

To give an example of where I am coming from, imagine a junior scholar's research area focused on "Diversity in Academia" (to use as an example). Within the past year, they have published in index journals on

economic causes of diversity
rates/trends in diversity
a meta-analysis on diversity
a large-scale experimental study on diversity

The university has positions on-

policies of diversity
economics of diversity
diversity in education

In other words, all of my research is applicable to those three positions so I am uncertain how I should approach them.

You imply this is a US institution you are concerned with. While only they can answer the question directly, and you should ask them, I think an application that covers all of the positions, would likely be acceptable.
I've assumed this is for a single department, of course, which likely has a single hiring committee. If they are hiring for three closely related positions then I'd think that they could decide which is a better match for yourself and themselves.
I would simply state my qualifications in an application, emphasizing elements that would be suitable for each of the positions. If you are interesting enough to them that they want to actually follow up and talk to you then you can refine things a bit, but I wouldn't try to guide it too much in the application.
In fact, I think a lot of places would find it odd to get three applications from the same person for a position in one academic department. That is so unless, for example, they indicate that there are actually three committees with three different chairs. In that case, you could send identical applications to the three chairs, mentioning that you have sent identical requests to the others.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is it a faux pas to not have your phd supervisor write a letter of recommendation as a post doc?
Here is the current situation I face:
I am currently a postdoc but have begun to apply for jobs as a faculty member for the 2019 academic year. My issue is in securing letters of recommendation.
My PhD supervisor is currently going through chemotherapy and I do not want to worry them with a letter of recommendation on my account. My supervisor seems to be taking a small break from academia during treatment.
My question is, for search committees, if my letters of recommendation include my postdoctoral supervisor but not my phd supervisor, will that be considered a faux pas?

I don't think the issue is etiquette, but rather whether they will think there's something suspicious about not including your PhD supervisor. If you've got other strong references, such as good coauthors or well-known academics from abroad, it might not look out of place.

When are the letters actually due? Further, your PhD supervisor may be quite happy to spend a bit of time doing something not related to chemotherepy, presuming that they are feeling OKish. (When my wife was doing chemo/radiation she really wanted to do something or think about something else whenever it was physically possible. It wasn't always possible, but...).

Have you talked to your advisor about whether they feel well enough? 2) Is it reasonable to ask for a letter of rec from someone from the same institution, and have them mention your advisor is medically unavailable?

If a few of my assumptions here are met, you might try the following. I'm assuming that you are at a different institution now (though that matters less than) and it hasn't been so long ago that you finished the doctorate that you aren't still remembered at the old place.
Ask the Department Head at your degree granting institution to provide a letter that says that Dr. X is not currently capable of writing letters of recommendation due to medical issues that may or may not resolve positively. If the chair him/herself can attest to your good work, that can be added as well.
The Head may actually more comfortably correspond with your advisor to see if this, or some other, solution is possible.
The point is that the letter should come from someone official. It should give minimal details (privacy reasons), and should indicate that a letter may be forthcoming if possible.
There is one other thing the Head might also be able to do in a large department, depending on its organization. If there is a secretary who normally handles that professor's correspondence, he/she may be in regular contact and so a letter might actually be very possible. But again, if the request comes via an official request you can maintain your respectful distance while the advisor heals.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Switching theoretical base for Ph.D. studies
I have a Master's Degree in a Humanities/Social Sciences discipline. I'm interested in pursuing a Ph.D. studies within this discipline.
My Master's thesis had a Posthumanist theoretical base. Would it be possible to so to speak "switch lanes" to a methodological-theoretical perspective more aligned with Culture Studies/Sociology?
I do understand that this all depends on circumstances and University orientation, but would it be possible to give a general answer to this question?

Most of the time, research "resets" between a master's and a PhD, and you are not obligated to continue your research focus between different programs.
(Besides, some faculty change their "base" several times during a career—why wouldn't they let students do the same?)


text:
SoP for applying CS PhD program with research experience that is not my interest
I am applying for a CS PhD program in the US, next year, as an international student. I will complete my CS undergrad in a few months. I already have research experience  with my project advisor. Also, I did a research internship at another well-known school with a similar topic. This project was presented in an international conference, too. I think this should be beneficial for my application.
However, I am not that interested in my research topic. It is related to computational neuroscience. At first, I just wanted to gain experience working with Machine Learning but I did not have an idea what problem I should be working on. Neuroscience sounded interesting to me, so I picked that sub-field. I did apply ML in my research project as I wanted but the neuroscience stuff was definitely not my thing. It has been an exhausting time for me to work on a project I do not like. I am still OK with ML and I am passionate about it. The thing is that I want to get away from neuroscience when I apply for a PhD. Right now, I have an idea to work with ML on low-power IoT device (such as camera) but I still have time to think about it thoroughly.
The question is that how can I write a strong SoP in this situation? If I write all about ML & neuroscience in my SoP, I am afraid that I will end up in a lab that I do not like. On the other hand, if I mention ML & IoT, I may have a weaker SoP since I have no experience in this sub-field. From my understanding, SoP is not a commitment but I am not sure that this will affect my journey or not.

In my own SoPs I wrote about my past experience and how it informed what I wanted to do in the future. For me in particular, I had done some computational research and some bench work unrelated to neuroscience, but I wanted to do some more wet biology in neuroscience. I wrote about how those relatively unrelated pieces of experience would apply to what I wanted to do next. I think it makes a lot more sense in a statement of purpose to talk about what you want to to study and learn rather than only what you've already done. If I said "I've been growing walnuts my whole life and I want to do this PhD to grow more walnuts" - that might be great in a job application to be a walnut-farmer, but if I read that in someone else's SoP I'd wonder why they were after a PhD and if they had any idea what a PhD actually was.
Presumably in your work with machine learning in computational neuroscience, you've learned about some of the benefits and limits of machine learning in that domain. You now know a bit what it's like to work with those tools, and you'd like to apply them to a new problem. Presumably, in a CS PhD, you'd be expected to do more work developing the tools rather than just applying them. That seems like a pretty straightforward SoP to me.

For CS doctorates in the US, you don't normally need to come with a research topic. This is especially true for someone coming straight from an undergrad institution. You can start fresh. (Note that "undergraduate" has different meanings in different places.)
However, if you apply to a program that, itself, has a strong neurological science focus then you will probably get stuck there. But there are a lot of possibilities outside that area. Most such US programs expect incoming students to have a broad education with some focus on a field, but not an especially narrow focus.
Make your SOP forward looking for the most part. The CV tells what you have done already, make the SOP about what you want to do: Machine Learning or whatever. Talk about why you can be expected to succeed in the new endeavors.
In some other places, students may need to already have a strong research focus to begin. That isn't true here. Expect that most PhD programs will include some coursework.


text:
How to search private annotations in Mendeley?
I have dozens of papers in Mendeley. Most are filled with post-it notes, what Mendeley calls "private annotations". Unfortunately, these are not searchable.
Mendeley users have been asking this feature for years. It still hasn't been implemented.
There is a workaround: exporting the article as PDF. The private annotations are added in pages appended to the PDF. But it is tedious: it requires to manually export each and every paper one by one...
I know Zotero's annotations are searchable. So I exported my Mendeley Library to Zotero. But the private annotations don't follow. Furthermore, Zotero only has a 300 Mb capacity, whereas Mendeley offers 2 Gb. So back to square one.
Would anyone have found a way (maybe a programmatic way) to search Mendeley's private annotations?

Just use Zotero Standalone with your PDFs database synchronized to the cloud of you choice (e.g. Google Drive, MEGA, DropBox...). For better file management, use ZotFile. Basic idea is to separate meta-data from PDFs. Meta-data are synced to Zotero account, and PDFs are synced to your cloud.

You CAN search your notes from the library/folders page (searches all notes for all documents) by selecting "Notes" on the drop-down menu in the search box. I don't know why you can't search notes from within a specific file.

As far as I can tell this only searches within General Notes, not Private Annotations

There is a tool for exporting the annotations from the whole Mendeley database: Menextract2pdf.
From their github page:

Menextract2pdf extracts highlights and notes from the Mendeley
database and adds them directly to all relevant PDF files, which can
then be read by most PDF readers.
Why? PDF highlights and notes in Mendeley are stored in the Mendeley database and can not be read by other programs. While it is
possible to extract and save the annotations to the PDF file, this is
a tedious manual process requiring to open every PDF and selecting
export to PDF for that file. Menextract2pdf provides a bulk export
functionality.


text:
Do published papers always have to present an innovation?
I would like to publish a/some papers online. But do the things I discuss in these papers have to be innovations. I am still a student and would like to publish a paper about aerospace engineering (especially attitude determination, control systems for satellites, GNC systems).
Those are not the easiest topics, especially as I am doing that alone on a voluntary basis. So does the paper I will publish have to discuss any innovation? I think publishing something where I explain how some algorithms work, which I tested my self, is much more doable. I could then just explain the algorithms (which already existed) and present their results. Would the latter still be considered as a decent (research) paper?

If you query the literature and find there's not been a decent critical review in the last ~3-5 years, you could viably review what's currently out there and use that knowledge to propose a novel direction for future efforts. Normally a research paper will have to put forth novel content/ideas/algorithms, or build on an existing idea in a novel way, like taking that predictive algorithm and improving it's efficacy markedly.

Online you can generally publish whatever you want, unless you would like to publish in a specific venue. But who is your target audience? Given this other question of yours, if you want to publish a paper online to increase your chances to be admitted to a PhD program, this would quite probably not work. Admission committees typically consider only papers published (or sometimes submitted) to known conferences and peer-reviewed journals (stay away from the so-called predatory journals).

@MassimoOrtolano, so a place like "researchgate" isn't ok? I am just a student doing that on my own, how can I get  published in such conferences or peer reviewed journals? + there are almost no conferences about the area I am interested / Willing to research. My target audience anybody who wants to read my paper. The main goal of my publication is to get accepted to pursue my PhD.

No, ResearchGate is not ok if you want to increase the chances of being admitted to a PhD program, at least in many countries. If you want to publish, really, join a research group in your field for your master's thesis: make it clear that you want to do a serious work and that you aim at being admitted to a PhD. Choose carefully the research group among those that are clearly active in their field and speak at length with the potential advisors about your goals.

The people who constitute the research group are mostly my teachers. And these people know my grades...(which are average) . Why would they accept me? I think it might be more interesting to do something which they are not aware of and then a litlle before I graduate say something like " hey have you seen everything I 've done? Without u knowing" So I d like to use that as a great surprise argument, so they can't say no. I u know what I mean?

And just just joining those people for my master thesis might not be that interesting.  I'd prefer doing a lot of stuff before my master thesis. So I already have a bunch of arguments and prooves as why they should allow me to pursue my PhD. And on top of that I'd like to add the fact that I joined a research group for my master thesis.

@privetDruzia I'd happily accept a student who shows genuine interest. But I'd look at their academic performance carefully, I won't take on somebody who will end up failing or otherwise be harmed by spending time on non-class activities.

Doing research is like almost any other activity: you learn by doing, by making mistakes and having a mentor correcting you and leading in the right direction, pointing out interesting problems, explaining what has been tried and didn't work, discuss possible aproaches. Going alone won't get you far (or even anywhere)

@vonbrand so where could I publish a paper before applying for a PhD in order to maximize my chances of being accepted? (As research gate doesn't seem ok and there are almost no conferences about the domain I'm interested in) I'm very motivated, but need a few tips in order to keep doing the right things so I can be accepted.

I would be more convinced by someone that collaborated with me or a collegue rather than a "surprise performance" when hiring potential PhD students. I particular because the quality of stuff produced by students on their own is usually (far) less impressive than they think. In principle that is OK: what would the value of a PhD education be if you could do just as well without one? However, students learn a lot more about doing real research from collaborating in a team, and those that learned more are more likely to do well in a later PhD program.

@MaartenBuis, So should I try to find a way to work on some project with a teacher before applying for a PhD (and before starting my master thesis) to increase my chances? Even if I will only graduate in one year and a half (if everything goes well)? But if I have a full-time schoolschedule those teacher might justg answer me: "How the hell would you like to work together with me if you have class every day from 9-5".

That depends on the local circumstances, so I cannot comment on that. All I can say, that I employ students in this form. They don't safe me much time, and I don't expect them to: It is basicaly an internship, though it is not called that way in my institution.

@MaartenBuis, Thx! I ll try that! asking whether it is possible to work on a project (next to my compulsory courses)is supervised by one of our teachers during the time I am studying an not yet accepted for a PhD.  + I ll do my best to find a way to publish at least one paper.

do published papers always have to present an innovation?

Not really, it has to make a contribution to existing understanding, and this  can be a very specific contribution in a very specific area. Look at this paper for example:
Gauthier, Joseph P., Eamonn P. Glennon, and Andrew G. Dempster. "Timing Performance of V2R3 Namuru Operating in Position-Hold Mode." (2013).
It provides a very useful, but very context specific, contribution.
Of course the problem which you will face in trying to replicated a paper like this is that unlike these authors, you lack equipment and data to write up such results. However, you could consider getting data from one of the research laboratories working in your area and trying to publish something with them. This could be something where you write up some part of the analysis, or, if you really know your stuff, you take the data they have and then do your own analyses. More likely than not you would have to cite them as you are building on their work/collected data and efforts.
Another option for you would be to do some sort of literature review, for instance, timing performance for GPS satellites: A review of the literature. Something like this would also qualify as a contribution and could be publishable. Plus, if you did it in an area where you would like to do research, it would serve to signal that you are serious about that research and also happen to know quite a bit about it.


text:
Citation and reference to a figure: which comes first?
This may be a bit of hair-splitting, but maybe there is a proper way to do this: In my thesis I present an external application. I want to give a literature reference to the application and a reference to a screenshot. What comes first, the literature reference or the screenshot reference?

The SuperFramework [1] (cf. Figure 1.1) ...

or

The SuperFramework (cf. Figure 1.1) [1] ...

Figure 1.1 is the screenshot.

I don't think there's any way to stick a citation and figure reference right next to one another in a non-ugly way, so I cheat.  When faced with a situation like this, I reorganize the sentence so that they are separated, e.g.:

The SuperFramework [1], for which a screenshot is shown in Figure 1.1, ...

If you have to go with either (and not with what jakebeal suggests), I would go with the first option:

The SuperFramework [1] (cf. Figure 1.1) ...

I'm afraid I don't have any reference for this, it's just my copy editor hat on.

I agree with this. Placing the citation after the figure reference might give some readers that the citation is the source for the figure rather than the framework.

@Significance A source for a figure should be mentioned in the caption, not in the text.


text:
Can we use a book figure/illustration in a review article and cite the source without getting permissions?
I included two figures from book in review article. I emailed the editor and author of the chapter for permissions, but they didn't reply. I also mailed CRC publisher for permissions, but still didn't get response from them.
If I still use those figures in a review article and cite the original source, will it be legal or not?

In general, just because someone doesn't reply, doesn't mean you can do whatever you want.

then how to tackle this problem?

How long did you wait? To obtain the permission to include a professional's photograph in a paper, we once paid a nontrivial sum (not huge, but nontrivial). That being said, that photographer of course makes his livelihood from these photographs, while a scientific publisher most likely doesn't and one might be hopeful that they would more permissive in a scientific context - but you cannot count on that. See the case of Eric Weisstein vs. CRC.

You cannot publish somebody else's copyrighted material in your own documents without a license.  Typically, the copyright is held not by the authors but by the publisher, e.g., CRC Press.
For most large publishers (including CRC Press, which appears to be owned by Taylor & Francis), they have a standard procedure for obtaining permissions for republication, e.g., to include a figure as part of a review article as you wish to do. Depending on the particulars, sometimes it will cost money and sometimes it will be free.  In any case, sending email will generally be pointless because they will expect you to go through the standard permissions process instead.
In this case, if you go to the CRC Press permissions page, it leads you to a general copyright licensing service, which has a "pay per use" system for obtaining, among other things, a license to:

Republish an article, book excerpt or other content in your own books, journals, newsletters and other materials

Finally, note that it is sometimes worth checking whether an alternate free version exists.  For example, authors may have also previously included similar material in a US government report or other item where you can freely use the material (always with appropriate attribution, of course).

if i redraw the illustrations and cite inspired source then still do i have to obtain permissions?

@ZeeshanKhalid If you almost-exactly recreate the illustration, then you would still need to obtain permissions.  If you recreate with the same content but in your own distinct organization and style, then you only need to explain your source and cite.

@BenCrowell While you're right about the existence of the fair use, this legal doctrine is perceived by many (myself included) as a last resort option. However, in addition to fair use and normal procedure, outlined above by Jake Beal, there is a third option. For books, published under Creative Commons license, I think that it is legal and academically ethical to (properly) cite artifacts from such publications without getting specific permission (provided the paper citing that publication matches conditions of the license, e.g., CC-NC-licensed artifact is not cited in a commercial outlet).

Note that for many large publishers (though not CRC) there is a reciprocal permission scheme - you need to ask as a formality but costs are generally waived. Participants - http://www.stm-assoc.org/copyright-legal-affairs/permissions/permissions-guidelines/

@AleksandrBlekh Actually, a CC license (or other similar open license) is specific permission to use artifacts under its terms.

@jakebeal Sure, it is. What I meant is that, because of that fact, people don't have to make efforts of obtaining permission, such as the case for non-CC-licensed copyrighted materials.


text:
Revision letter and grammatical errors
I got a major revision and I will prepare a revision letter. The editor asked me to review my manuscript for grammatical errors, in addition to the scientific comments he made. Should I present all the grammatical changes I made on the manuscript one by one? There are lots of minor changes (i.e addition/insertion of commas, "the", "a/an").

I recommend providing a red-lined version which shows all revisions. This can be done automatically.

Since they haven't pointed out what mistakes you have, it is unlikely they have a list of errors they have found; therefore, enumerating your changes is pointless. Also, since you got "major revision", a good chunk of your text should be changed anyway.
Just make sure you double check the language before resubmitting, preferably by someone else (native speaker would be ideal).

Should I present all the grammatical changes I made on the manuscript one by one because there are lots of minor changes (i.e addition/insertion of commas, "the", "a/an")?

This seems unnecessary. What I usually do is report all the mentioned grammatical errors, and then just remark that I fixed all of them.
That being said, if there are so many grammatical errors that this is an actual problem for you, you definitely need to tighten up the writing of your paper.

I very much doubt they care for you to acknowledge every problem they point out to you, they just want you to fix them (and others you might find in the process). If you disagree with some of the suggestions, then it makes sense to speak up and explain your reasoning (should probably do it in the text too, if whoever did the revision didn't understand it, chances are it will confuse other readers too).

You can submit two versions -- one with Track Changes turned on, showing all the changes as edits, and one with all the proposed edits 'accepted'.


text:
First paper published, follow-up paper rejected by editor as out of scope?
I published an article few months ago in a journal. I sent another article to the same journal, in which I improved the design idea and enhanced the computation.
I was told that my second article was sent to Prof. X (name was provided) as a topic editor.
After about 70 days, I got an editorial rejection due to the article not being within the scope of the journal. In the online submission site, it said that my article was under review for the last 70 days.
In the end, my article was not even sent to referees... is that normal?

Yes, it is normal that articles get rejected as not in the scope of the journal. Yes, it can take a long time for the people in charge (often doing this pro bono) to get around to take a look at an article.
So you published something related before in the same journal. OK, maybe they just want "new results", not the elaboration/extra details on previous ones. Or they don't want "enhanced computation" (presumably more detailed results), and prefer description of methods. Without an awful lot of additional information, we can't tell. Besides, whatever the case may be, the powers that be at that particular journal have the last say. If we consider it normal or not, is totally irrelevant.

Actually, my second article to the journal has a new design for the same device, and some improved calculations of the mathematical model. The main issue is that it took them 70 days for editorial rejection which was suppose to be after 10-15 days. Also, the journal website should not say it is under review if it is not even sent to a referee. These are miss leading and inaccurate information that lead to more delay in publication process....

@zoweil referees are not the only people who review which is information included n the answer. Editors are also often involved.

It's absolutely normal to experience some degree of inconsistency in how a journal judges its scope.  From what you have described, it seems likely that both of your papers were somewhat borderline, and the first editor made the judgement call one way while the second made it the other way.  That's entirely normal and reasonable, because judgements differ between editors, no matter how consistent one might attempt to be.
What's not normal is being forced to wait 70 days for a desk rejection.  In my experience, editorial rejection is typically very fast, within a couple of weeks at most.  More than two months time is enough for a full peer review.

I was complaining about the 70 days period, for a decision that takes only 10 days, beside this I did not even get a feedback from any referees. Rejection is ok, but not getting any feedback from referees that is not ok after this long time....

@zoweil I agree: the edit should not have sat on the article for 2+ months.  Unfortunately, some journals are not very responsible about their workflow.  The best thing to do is to avoid those journals, if you can.


text:
What's the best way to justify your choice of baseline methods for academic paper?
As the title states I'm curious how to justify the choice of baseline methods for academic paper when proposing a novel algorithm/method. For example, when proposing an algorithm, there is a suite of methods applicable. When I choose one method to compare my algorithm to, how do I justify it?

Welcome to Academia SE. Can you please specify what you mean by baseline method? Also, if I am guessing correctly what you mean by that, I find the question rather difficult to answer except in a maximally fuzzy way, as it always depends strongly on the actual reason for your choices.

The justification of the methods you use should start well before the paper - what did you do, and why did you choose to do that rather than something else?

I believe that OP could clarify, but they have a new method that they want to compare against a baseline and are curious about the best way to find which baseline to compare against. In my field(s) this would be the fastest, most accurate method already published.

You may lift the hold. The question seems pretty clear to me. Eg., if there are a list of classifiers in machine learning (RBF, ANN, GA, SVM, etc.), and you choose one, how to justify your choice of algorithm?

When you propose a method in a research paper, it is customary to describe how you came up with the method and why choose it over the others available in literature. There are a few tips you could follow to justify your selection.

The traditional way to do this is by doing a thorough literature survey of all other methods assessing the advantages and shortcoming of each and then show how your chosen method could probably supersede those methods.
Sometimes you may find many such methods that are applicable but for which you cannot find existing results. In such a case, the best thing to do is to produce results for all of those methods and select the one with least drawbacks and most desirable merits. If the amount of publishable work exceeds your paper limit (or if your time is limited), choose one among such methods for your current publication, but discuss the other methods that can also be applied that could be of scope for future work for research.
A few journal publishers would also welcome negative results (such as PLoS ONE). Hence you could assess a method and show how suitable/unsuitable it is for a certain application based on the results.