text:
Should I apply for financial assistance to go to conferences?
Many conferences offer some form of financial assistance, covering travel, registration, accommodation, or combinations thereof.
My university will only pay for one conference travel expenses over the course of my PhD.
While I live in a first-world country, I am not financially well-off. I can't easily afford to fly to conferences in my own country, let alone some of the more exciting international conferences.
A lot of conferences I am really interested in are of side-note to my research -- things like SciPy. Or conferences from related fields.
Is it worth me applying for financial assistance in these cases?
Or is financial assistance restricted to people from developing nations,
or to people researching the primary area of the conference,
or to people who are submitting papers to the conference?
Is the paperwork involved generally long and complex?
it is not worth the time to spend a week filling out forms, for a 1% chance of getting to go the a conference -- I could be spending that time on actual research.
Are these awards highly competitive?

While your university might only pay for one conference, often times travel is budgeted for by principal investigators when writing grants to support their research. So you should check with your advisor to see if she has funds available to help support your travel to conferences beyond what your university is willing to fund.

Is it worth me applying for financial assistance in these cases? Or is financial assistance restricted to people from developing nations, or to people researching the primary area of the conference, or to people who are submitting papers to the conference?

Every conference has its own specifications for what kind of applicants (if anyone) is given preference for travel grants. Sometimes paper authors are given preferences, sometimes they are de-prioritized. Sometimes participants from underrepresented groups (whether in an academic, racial, geographic, etc. sense) are prioritized and sometimes only US citizens are eligible. Refer to the conference website for details.

Is the paperwork involved generally long and complex? it is not worth the time to spend a week filling out forms, for a 1% chance of getting to go the a conference -- I could be spending that time on actual research.

No, it's not usually long and complex. Generally it involves some or all of the following: a statement from you on why they should give you a grant, a letter from your advisor indicating that your attendance will be to your benefit and the conferences' benefit, and an estimate of your expenses.

Are places highly competitive?

Depends on the conference. Conferences that many people want to go to tend to be more competitive.

Another option is to get external funding for conferences. There are some programs for funding student travel to conferences, particularly (or mostly) for underrepresented minorities (including women). For instance, in Computer Science, the ACM-W offers conference scholarships to female students, for any conference. If you are a woman or minority, try searching a bit to see if you can turn up a scholarship in your field whose criteria you fit, and/or ask your advisor and other students in the department if they know of any. Even if you're not a minority, you can search a bit to see if you can find anything. These are often somewhat competitive, but the chances are usually much greater than 1%, and there isn't that much effort involved.


text:
Can a professor I didn't mention in my application accept me as his M.Sc. student?
A professor that I contacted earlier as a prospective student replied to me (and asking for interview) late when I already have submitted my application. I didn't mention him in my application, since I thought he might not be interested and deadline was near and I mentioned other professors who replied to me. If the interview is successful, can he still review my application and admit me under his supervision?
Note: I can't edit my list of Professors on my application, but I can still edit my SOP (maybe mention him only in SOP?).

The simple answer is: yes.
At many schools it is often the case that professors discuss the applicants outside of the official application system. Other professors may have recommended your application to the professor in question, which is why they are asking for an interview with you now. I suggest you concentrate on doing as well as you can for the interview.
Don't worry about the details of their internal process - you don't have any control over that. If the professor wants to work with you, there is usually a way to make it happen.

source: Stack Exchange

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/

sort: votes


text:
How to be confident that my background for my research is adequate?
I am a third-year PhD student in Computational Algebra with a B.Sc. in Computer Science.
While doing my research, I often need to check my old textbooks for definitions, and I am concerned that I may not be adequately prepared despite having done the course work seriously.  Due to this to me I feel like I should read a textbook for 2 weeks then start doing the research.
Others have suggested to only read a book when you need a particular lemma/proof/etc., however I am conflicted on whether this is good advice.
Question:  What should I do?
Please note that my supervisor told me that you know enough for research. Is this kind of feeling common among PhD students?

This kind of feeling is the definition of being a PhD student.

This kind of feeling is the definition of being a researcher.

To add a grain of salt: this is one of the major reasons for the imposter syndrome. But yeah, "crap, I need to read up this" is a normal feeling.

If your primary symptom of concern is that you lack an encyclopaedic knowledge of your subject matter then I wouldn't worry - it would take a rare specialist with a very special brain to have that level of knowledge of an academic subject.  Checking definitions is common in research and it is rare to memorise academic material in a level of detail that would render checks unnecessary.  For most academics it is usual --over time-- to develop a solid knowledge of key concepts and results, with the ability to check more tangential matters, or particulars of definitions and proof, by reference to academic texts and papers.
The best thing you can do is to prioritise the importance of concepts and results in your field, and try to commit important core concepts and results to memory as well as possible, while making note of where you can get information you are likely to forget.  Unless you are going to become a specialist mathematician it is generally unnecessary to memorise proofs of theorems, and even for people in this category, they might know a few proofs off by heart, but for most they will remember that a certain technique is used, without remembering all the details.  For mathematical work it is useful to remember the substance of important theorems and remember the techniques that are applied to prove them.  It is perfectly okay to forget the exact conditions of theorems or the exact details of proofs, but if they are really important, you should try to remember the substance of them, and have the capacity to find the details when needed.
Over time you will find that you learn your field more comprehensively and you become more used to the methods and techniques used in that field.  For a mathematical subject you will usually find that most things are proved with variations of a relatively small kit of proof techniques, and you will start to recognise them well enough that you can remember roughly how to prove things without much cognitive load.  As a result of this you will find that you can absorb material faster and so it will become much quicker to refresh forgotten knowledge with textbooks and papers.  A refresher that took you two weeks at the end of your PhD might take only a single morning once you are an experienced researcher.  That takes time!

This is definitely a normal feeling. To address the feeling of not being prepared, you might want to realistically revisit where your skills and comprehension were a few years ago. If you can feel the progress you have made already, you may be more likely to believe that you will make the progress from the confusion you feel right now to having defended a dissertation.

Do you ever have a chance to tutor undergraduates in upper-level classes? Could you sit in on an instructor's office hours for classes you took at the end of undergrad? This might help you see that you have made a lot of progress.
It may feel like your colleagues are ahead of you. You might have a few of them who truly are, who know their own specialty and everyone else's specialties at an expert level. If you look at the rest of your cohort who are not doing Computational Algebra, though, you probably know more about the details of your field than they know about it.
You can remind yourself of what you do know. Map out some of the big concepts that are related to the work you want to do. Actually draw a picture about how ideas link up. This can be half brainstorming, and half a chance to see that you have a much broader knowledge of your area, and how things fit together, than you used to. (You can come back and do this at the end of every term, perhaps, and you'll see how your picture changes and grows.)

You've chosen to surround yourself with smart, talented peers and professors. Comparing yourself to them may make you feel like you're behind, but comparing yourself to yourself will remind you of your ability to learn and grow.

Yes, it is common and it is completely OK. Here is an article that is worth reading: The importance of stupidity in scientific research.

Your research answers a few questions about a certain problem. In other words, you are giving one or more solutions to the problem your research is all about. When you have enough answers to these questions or problems you are done.
On the other hand, reading the whole book is not wrong for learning to be more confident about basics in your field. What you read more serves you as a researcher in a certain field. Therefore, the more you read, the more you become expert and have good background. But for Ph.D. you only read what helps in answering or solving the problem you aim to solve in your research.
Hope my answer was helpful.
Have a nice day!

A number of these mistakes due to speed in writing

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/3.0/


text:
Is it okay to file administrative complaints about problems with the facilities and services in an academic settings?
Background Information:
I am a doctoral student at a premier institute which is also a hospital. Most of the administrative positions are handled by professors who are also clinicians and researchers. Sad as it might be, there are a lot of things for which the bar is quite low. Three specific examples:

the cafeteria on campus has absolutely rock-bottom level of quality/hygiene standard
similar low standard when it comes to maintenance of washrooms etc.
impossibly poor standards of on-campus residences

These are usually taken care of by administrative staff but at the end of the day are under administrative control of one or the other faculty (honorary "in-charges"). Not only these set a very poor impression when we have visitors but it also lowers the morale of the research staff. Sustained exposure to such a pathetic environment impairs productivity and there is always a prevalent air of gloom among students on the campus. Somehow it seems that the administrators are not interested in remedying any such situation and things seem to have become worse in the recent years.
Question:
Is it potentially harmful* for students to send formal complaints to the administrators requesting action to be taken? In case the administrator does nothing, should it be sent higher up in the hierarchy? How should attention be brought to such things so that they are resolved?
*harmful in terms of being bullied by senior faculties in the future; having carrier plans blocked because the same faculties might be on your review committees, et al
What I have tried to do:
I have sent anonymous emails to which I have either not received any reply or else have received a reply explicitly asking me to disclose my identity. In either case, complaints have never been worked on. I have tried to speak to my advisor about this but he has never been encouraging about the idea of formally writing complaints because of similar concerns mentioned above.

I don't think this is a question the Internet can answer for you.  It depends on your particular institution's culture and the personalities of those in charge.  We have no insight into that.

Sorry to hear about your troubles though - I would suggest talking to someone local whom you feel you can trust.

Potentially harmful?  Yes, anything is potentially anything.

Do the problems also influence patients at the hospital, or are their washrooms all clean and only the ones for staff or in the student residences are dirty?

The maintenance is sort of just okay; there are no facilities as such: tissues, sanitary napkins, liquid soap (only solid non-disposable soap that everyone shares), etc. Since this is a government setup with extremely high load of patients (and where most of the patients are from poor socio-economic background) just basic cleanliness seems acceptable to the administrators. In comparison to other government hospitals, the standards might seem high (which is what tends to be a benchmark for the administrators); imagine the horror experienced by international visitors to research site though!

Your best bet is to use safety in numbers: a single complaint won't lead to much of a response and may cause some friction for you in the future.
If you can organize a large number of students to complain, though, it may be possible to achieve much stronger results. Moreover, it is unlikely that the administration will be able to retaliate against a large group at the individual level. (You might not want to be perceived as the "ringleader" if you are worried about possible repercussions.)


text:
What is the "goal" of the PhD?
I am little confused about the goal of PhD in the middle of my PhD. I used to think that PhD is equal to Research but in the middle of my PhD I find out that it is much more than only research. It involves TA work plus some other academic work and research also. Before joining the PhD my goal was to publish something revolutionary during my PhD but I believe that PhD is a process in which you do three things ( according to my seniors )

Work on some problem you find interesting
Write and submit to some conference
If rejected again submit after modification

This is a typical PhD process. The above three steps will help me to get me a PhD, but it does not let me make a significant contribution which will help in finding job after PhD (postdoc, etc.).
Question:  What is the "goal" of the PhD? Is it more than the above three mentioned steps? How to ensure that at the end of PhD I will have something significant research contribution? Do I only need to worry about this or my research supervisor also?

My opinion: A Ph.D should evolve you into a professional researcher. Having a Ph.D is an indication that you can successfully understand a potentially large research topic to that amount, that you can contribute to it and keeping it "move forward". It also makes you the worlds best expert in a very small topic(your dissertation)

http://matt.might.net/articles/phd-school-in-pictures/

To that I may add that a PhD is your formal first step towards being an academic. Of course, some may (and many do) go to private industries but for a large number of PhD students - it is with this goal in mind.

A PhD is about research. Of course, there are some other things - for example, in some universities you have to take classes because it is assumed that they help you with your research. TA is - in the universities I know - necessary to get money. Some supervisors also see their PhD students as their assistants and assume they help them with things not related to the research (e. g. with teaching, without compensating the student).
The goal of a PhD is to write and defend a PhD thesis. If everything is done correctly, this implies that the PhD student has substantial knowledge about her subfield and has made a groundbreaking contribution (but the ground that she breaks may be small!) Moreover, the student should learn in her PhD to be a professional researcher. This includes things like publishing, going to conferences etc. Those are then the things a PhD graduate will be evaluated on if she applies for academic jobs.
Your supervisor should, of course, also help you to become a successful researcher. However, it she does not care about you, the only thing you can probably do is to change your supervisor. However, you being successful is also good for her career.

What did I do wrong? Please explain, downvoter!

The goal of a PhD is to make a contribution to the body of human research. This involves, not only doing the actual research, but reporting it, too. And it can involve verifying the research of others, because any real research should be verified by peer review.
Writing publications is the process by which research is reviewed and reported. A series of smaller publications is less risky than one big one, especially for a new researcher, but it is not unheard of to present all the work from your thesis in a single peer reviewed publication.
You cannot always do research in a vacuum. At the end, to have impact, someone must at least read the research. Your PhD will be judged on your novel contributions to your field and these will be that much stronger if they are peer reviewed and published (or in the process of such).
Answers
The aim of a PhD is to make a contribution to research. It is more than having papers submitted (accepted), your papers should report the results of your research so your peers can review your contributions. Peer review will validate your contributions, ensuring their significance and correctness (or plausibility). It is YOUR research and it will result in YOUR thesis and YOUR contribution (or publication list). But I’m sure your supervisor will correct you or point you in the right direction if you go astray. As far as a job afterwards is concerned, academics are judged on their impact factor, which is often based on their publications. Some (industry R&D) places will use a PhD requirement to narrow down the candidate list and ensure the ability to understand complex problems and educate yourself.
In my field (Computing Science), I’ve seen some thesis where each chapter has been published as a paper: a review paper plus two or three experimental papers. I’ve seen another which resulted in a single journal paper covering most of the thesis, but if you spend years gathering a dataset, the major contribution is the dataset itself, not the publication that describes it (although that’s important, too). Some advice has been to view the thesis as a series of sprints rather than a marathon and "publish or perish".

The goal of a PhD is to make a contribution to the body of human research. — I disagree.  The goal of a PhD is to learn how to make a contribution to the body of human research.  The purpose of a PhD program isn't to produce research but to produce researchers.

I hear and I forget. I see and I remember. I do and I understand.. A successful PhD thesis will make a worthwhile contribution to research while developing the student as a researcher.

Of course, it's impossible to become a good researcher without doing good research.  But it is possible to produce good research without developing the knowledge and skills and habits required to continue as a good researcher.  The goal is not to make a painting, but to become a painter; not to win one race, but to become a runner; not to kill one bear, but to become a hunter.

The goal of a PhD depends on who you ask. From your advisor’s perspective it is to prepare you be a competent, accomplished academic that will be competitive on the job market - including research, writing, mentoring, teaching, etc.  But, this need not be your goal. Perhaps you plan to leave academia for industry. Perhaps you plan to take a teaching position.
The reason the above is important is that it gauges what ‘important contribution’ means. If your goal is to run a lab at Harvard, your contribution (publications) will have to be very high caliber (and probably numerous).  But this need not be satisfied in order to earn the degree - your department will have minimum criteria; some don’t even require publication.
Assuming you wish to stay academic, how do you ensure ‘significant contribution’?  By identifying holes in the literature you think you can fill, doing a strong study, and writing a persuasive article documenting it.
It would be nice if your advisor worried about this too, but the onus is mostly on you to push forward.

My experience so far being a PhD student is the following that somewhat attempts to answer your question "What is goal of PhD?"

It is first step towards starting a career in academics
It is far more than just publishing articles in conferences and journals
It is the degree which builds your team skills, time management skills
Teaches to learn to have patience
Teaches how to handle rejection
Reduces unnecessary egoism (or sometimes egotism)
Teaches to think and express in clearer fashion
At the end, provides the satisfaction at the end of the day (!)

I think you would find the book Advice to a Young Scientist by Peter Medawar useful.


text:
Don't last-year PhD students need supervision?
I am a PhD student currently in the middle of my PhD. After talking to some senior PhD students, I came to know that during the last or second to the last year of PhD, advisors don't advise their students (advice to very small extent ). There are many things last year students have to do on their own. I don't know if this is true or not in general.

Question : Don't last year PhD students need supervision?

You might clarify whether you mean advise on research &c, or advise on the process/paperwork needed to fulfill degree requirements.  My limited experience is that one needs much more of the second than the first.

On the one hand the amount of support needed on how to do research should decrease as the PhD student progresses. On the other hand, at the end is "crunch time" and a lot of projects come to an end at the same time. Each project should require less support by the advisor, but now there are more projects to discuss... Moreover, there is the process of finishing the dissertation, ceremonies, etc. etc. So the amount of time I spent on a PhD student would follow more a U-shaped curve: a lot at the beginning, then decreasing, but increasing again at the end.

While my answer is specific to CS, might be general enough. After writing it, I noticed that I'm mostly focused on the writing, the technical parts were never an actual problem for me...

Personally, I try to decrease my involvement with Ph.D. students over time. The objective is for them to be independent researchers by the end of it after all.

First years usually require a lot of supervision and hand-holding. Often they don't really know what they want to do, or how, or how to properly write it.  I found that putting them to help as "middle authors" of more senior PhDs is a good idea so they get a sense of the process.
When they start writing "by themselves", I usually do not directly edit the text, but rather comment on the PDF explaining why I want stuff changed. Each review takes forever, but at least they should be able to extrapolate the rules and develop a "sense" for it...
By the third year, I fully expect them to "lead" a paper, but I still keep a close watch, albeit with less interference... I see most of what they do but intervene only when unavoidable. Most are starting to develop their own writing style there.
4+ should know enough by then to deal with their own issues and help the "lower" students, so they require minimal supervision if any. And they have a dissertation to finish. Except for a few "dissertation specific" details, I never had to touch the dissertation, especially when it is in the "collection of papers" format.

Of course, that is just the general lines. I had students leading papers as undergrads and hand holding on the fifth year of their Ph.D.s, each person is different, stuff happens, and the advisor needs to be on top of it to "personalize" the supervision.


text:
What does it mean if the status of manuscript changed directly from "editor assigned" to "reviews completed"?
I submitted a manuscript to a journal a month ago but the status was changed to "reviews completed" after "editor assigned," with nothing in between. What does that mean?

To be concise, brace yourself to receive a rejection.

My money would be on a reject after a quick technical screening by the handling editor.

It means that the reviewers have completed their work and submitted their reviews. The editor will now make a decision based on her judgment as well as the opinions of the reviewers, and you should expect to hear back from the journal shortly.

Thanks a lot, but directly the status changed from editor assigned to reviews complete. Usually it must be changed to under review after editor assigned and then it changes to reviews completed.

@R.Behmanesh Is it possible you just didn't check it while it was under review?

No, I have been checking.


text:
Is it OK to use "Group A, B, C ..." in a manuscript?,
I am currently preparing a manuscript which lies in the biomedical field.
My study has five groups, and their identification is a bit tedious to describe in a full term (something like "'abcd' medicine + 10mg of 'efgh' medicine group").
Therefore, In the results section, I want to maximize word economy by not directly lettering out the specifics of the group, but just referring it to Group, such as A, B, C, D, and E. I am planning to propose a table that clearly explains the initial letters (A, B, C, D, E) of the group and its specific descriptions in the materials and methods section.
However, upon my research, many articles just endured the inefficiency of fully describing the group whenever it has to be mentioned. Is this some kind of a rule that has to be kept when writing a manuscript?

At least use reasonable acronyms for the names that are easier to match to the full description than a random letter of the alphabet. Otherwise one has to keep going back to your table for every figure with labels. It would deter me from finishing to read, in the worst case. It might work for experts in the field that can easily keep the relevant combinations in mind, but I have to read a lot of stuff that uses this kind of things and it is very hard to remember all treatment groups when they have informative names already. With noninformative ones I would just forget which groups are there.

In general, on the biomedical field Latin letters (A/B/C or a/b/c) are reserved for the figure panels (e.g. "Figure 1 A and B clearly show..."). Typically, biomed articles tend to have a lot of panels per figure, so it is suboptimal to use these letters for anything else. It is much more handy for the reader, if experimental groups have human-readable names that are clearly defined in the method section. A little fantasy may be helpful. For example,

Group 1 - placebo control - "Placebo"
Group 2 - 10 mg Blabla drug - "B10"
Group 3 - 25 mg Lalala drug - "L25"
Group 4 - Blabla drug + Lalala drug, once per day - "BLI"
Group 5 - 20 mg Blabla + 30 mg Lalala - "B20L30 and etc.


text:
How should I highlight extensive changes in a revised manuscript?
I revised and resubmitted my manuscript (rejected with the chance of resubmission) to the same journal. I listed all my answers to the reviewers' comments at the beginning of the document. Later, the editor asked me to highlight the changes in the text to make it easier to track them. Since I almost rewrote the entire paper (I mention it in the resubmission letter), about 85-90% of the text would be colored.
I have two questions:

Should I fulfill the editor's request even if almost the whole manuscript turns into let's say red? I'd prefer yes.
Should I place color tags in the Latex source file, or should I highlight changes directly in the pdf file? Which of these or even other choices are the most appropriate?

I did not ask how to track changes in Latex. I would like to know if it is acceptable to highlight changes in PDF instead of Latex (the source files need to be uploaded as well). And if it is awkward to color almost the whole manuscript.

Ah, yes, you're right: I've misread the question. I now retracted the close vote.

I wouldn't touch the latex source, there's a good chance you'll loose track of changes and end up with two versions. Speaking from experience here. Colour the pdf.

You might wish to color the old text only and tell the editor that the new text is in black.

Just to check, are you positive the editor meant to literally highlight the changes, or to emphasize the major changes by adding a thematic overview/summary of what you did? The latter is certainly what I thought when I first read that sentence.

If the editor's already asked you to highlight the changes, then you should highlight the changes even if it's 85-90% of the text.
As for color tags, it's up to you. Both are equally good. I would highlight on the PDF since I find it easier to do, but if you prefer color tags that's just as good. Be sure to pick a color like red or blue - something that makes it easy to discern the changes from the rest of the text.

A text that is 90% coloured won't help the editor or reviewer.

I agree with @Karl. What about highlighting what did not change?

No, but it's what the editor requested. I would consider it pretty impudent if I directly request an author do something and they don't do it (without a very good reason).

It's a dilemma, and the one way out of dilemma is communication. Make it clear to the editor he's not going to like what he asked for.

That I can agree with.

Let's try to move away from the letter of the request, and focus on the need behind the request: the editor wants to be able to distinguish between parts that changed and parts that didn't. Highlighting the parts that didn't change satisfies the need behind the request. Explaining to the editor why one did it this way should be sufficient to convince them.

@Matteo I would make sure to highlight the explanation, then because, like all of us, editors are creatures of habit.

I recommend that you submit multiple files, which should fulfill the practical solution of submitting the more useful unmarked file for review while also explicitly fulfilling the editor's request. Specifically, I recommend that you submit:

The revised manuscript with no revision marks. This should be your official resubmission file.
The colour-highlighted PDF file in fulfilment of the editor's request: this should be an additional file for reviewers only. Since the editor requested it and you are submitting it as a supplementary file, there should be no problem even if it is 90% highlighted. Concerning your second question, I think highlighting the PDF is sufficient, if it is easy for you to do. However, if it is easier for you to highlight the Latex version (e.g. via diff), then you could do that instead.
The Latex source of your final version: You mentioned in a comment that you are required to upload this, so you should do so regardless. Concerning your second question, I don't see why you would need to highlight the Latex if you submit a highlighted PDF version.


text:
Are there hacks or smaller scientific search engines offering you context-sensitive/semantic search?
The many upvots on Gerrit's answer show how the majority of researches currently does search, filter, read scientific journals and books, as the best way, a context-sensitive search(X Algorithm near to Y algorithm near to Z database) is not available in scientific search engines to my knowledge? A lot of time has to be wasted for filtering out uninteresting content.
An google WEB search example would be:
etching AROUND(4) redeposition

Search hits will only show sites where etching is separated from redeposition by not more than 4 other words between those two. While many research papers often contain many keywords in intro and abstract of a paper (for retelling recent history in a field), which makes finding papers in a special context impossible (measuring effect X with method Y on material Z), in principle the AROUND(x) operator gives you this power back.
The problem is, google SCHOLAR hasn't implemented the AROUND operator, therefore I currently use it sometimes in google WEB search when searching papers (unfortunately only titles and abstracts are indexed by Google, but main body content isn't searchable) in a very specific context.
I'm really wondering if there are secret hacks for free (google scholar, scirus...) and commercial (ISI, scopus) search engines giving you the power of context-sensitive search, as it would make a lot of reading, searching, filtering, rating, sharing unnecessary.
My current way to solve this is downloading many highly-cited papers (withoud reading) as gerrit's answer shows and indexing it with my own desktop search engine (Copernic desktop search software) which has a similar operator. It really ticks me off, that a search technology that is available for years is not brought to the place where it would be most useful?! Maybe we should similar to thecostofknowledge just start to build our own search engines? There are some business reasons (traffic, downloads,..) that make the non-implementation of this operator in commercial search engines very reasonable to me...
So, am I missing some secret hacks or search engines that are near to context-sensitive/semantic search?

A citation based, context sensitive web-finder(search engine) would be interesting to implement!
Google's around operator looks typically like a Hamming Distance implementation between two strings loaded as vectors.

I know it's disappointing, but here goes: I am not aware of features allowing context-sensitive search in scientific search engines, with two exceptions:

Web of Science has a SAME operator, which matches “records where the terms separated by the operator appear in the same sentence”. Given that Web of Science supports a whooping number of 4 search operators (AND, OR, NOT and SAME), it is pretty safe to say this is sadly the full extent of its context-sensitive search features.
SciFinder attributes some meaning to prepositions, which have a role in restricting results to “closely associated” matches of operands. This basically means “same sentence” (details in the linked page).

Yes, these features are poor and we should hope for better search capabilities. At the same time, it's a start and it can be useful.

thanks, I've asked on cs.se what limits implementation of such an operator for full-text, as both Web of Science and Scifinder only seem to index titles and abstracts reading your links. But good to know at least Web of Science offers it for abstracts!


text:
How to greet when having a PhD panel interview?
What is the most proper greeting for when you enter a panel of faculty members for a PhD Interview, and what for when you leave? I'm in the UK, in case that's relevant.

Hi, and welcome to Academia.SE!  Can you please give some indication of what country you are talking about? Customs may vary greatly.

"Hello, my name is AgosGag!"

This seems to be unrelated to Academia, unless the OP presumes we have different greetings in Academic interviews than in any other interviews.

@J.J: This assumption can actually be somewhat reasonable. In some languages/countries, it is customary to address people with their academic titles. Likewise, academic institutions are among the few organisations that, in many cases, publish complete lists of their employees online (with photos etc.), which is quite unusual in commercial companies. Therefore, there might be some particuliarities in academia.

Pretend that the group of professors on the other side of the table are actually human beings and treat them accordingly.

@Davidmh, not that it is true, mind you ;-)

Assuming you're referring to the proper addresses of faculty members at UK institutions, the general form is "Doctor" for faculty members who are Lecturers (known as "assistant professor" in some other countries) or Senior Lecturers (known as "associate professor" in some other countries) and "Professor" for faculty members who are Readers (varies between "associate professor" and "full professor" in other countries) or Professors (known as "Chairs" in some other  countries.  In some UK institutions, the North American standards have been adopted, so it's not completely uniform.
If you're uncertain as to the academic rank of the person, defaulting to "Doctor" will not likely offend.  If someone is introduced as "Professor", then use "Professor" in such cases.
In terms of matters of greeting not related to the proper address of the members, there are no formalities upon entering or leaving that you should be concerned about.  A general "Hello" / "Thank you.  Goodbye" or any variant are perfectly fine.

Don't overdo it. Just greet them in general, not individually. If they are presented personally, say by the chair of the committee, just greet each one in turn courteously, like you would do in any other formal setting.

What "other formal setting[s]" are you thinking of?


text:
What is a typical teaching load?
Are four 3-credit classes a typical burden for full-time faculty? Assume all are in-person courses, no new preps, no new books, no TAs, 15-25 students per class, no research/publishing required, and committee work is required.

I moved the question to the front and added the clarifier "for full-time faculty", based on a line from the comments. If that is incorrect please edit.

What is your location and field? (Reposting my comment seeking further clarification; mods: please, do not delete this.)

Without further details this question is too broad, and I voted to close.

It's probably reasonable.  The teaching load for a full-time lecturer with no research responsibility tends to range between 10 and 15 units, equal to two or three 5-unit lecture courses, perhaps one more if some are 3-unit.  What constitutes a full-time load at any given school is largely dictated by the financial reality imposed by their average class size and, thus, the tuition revenue per course from which you and all the other expenses must be paid.  If their class sizes are really small, as they are at your school, they pretty much have to load up each instructor to make it work.


text:
Can faculty in the United States get access to your grades without your explicit consent?
Note: This question is aimed at "in general, in the United States, given the laws (including FERPA) and typical practices of US Universities".
I'm wondering if my schools' departmental advisers can give my grades to faculty members without my permission. Say a faculty member is talking to the department advisers about me. What is standard procedure here?

Closely related: https://academia.stackexchange.com/questions/84931/in-us-universities-how-much-academic-information-does-a-professor-have-about-gr/84936#84936.  Short answer: wide variation.  It's entirely possible that faculty could get your grades, or might already have direct online access.  No laws restrict sharing of grades within a university, so long as it is for educational purposes (which includes almost everything).

Data point of 1: I can access the grades of any student that is attending / has attended my university. (So, e.g., when you go talk to your faculty advisor, and they ask you how things went last semester, just tell them the truth.)

Faculty are almost always bound by rules governing their access to student records.  For example at my university, I can access any student record on campus if I have a justifiable reason. If I were to access student records that I didn't have  justifiable reason for accessing that would be a major violation of policy.

I'm wondering if my schools' departmental advisers can give my grades to faculty members without my permission.

Yes.  The school's own policies will determine how, when, where and why.  Your permission is never required for communications about you within any school between faculty, staff and officials as long as it is pertinent to their job.

Say a faculty member is talking to the department advisers about me. What is standard procedure here?

The procedure is school specific and will usually be spelled out in either the faculty handbook or employee handbook.  You will not be able to access either of these as you are neither.
It would be unusual for faculty to not talk to advisors about students, although that partly depends upon how the role of "advisor" is defined.  It is common for faculty to be required to provide to advisors any form of academic warning regarding students.  Let me give you a simple example.  Imagine you were taking "Introduction to Microeconomics," and were struggling with the algebra.  In many schools, the professor would inform the advisor that the student should take appropriate math courses in future semesters.  How can they give advice if they do not know what is going on?
It also goes in the other direction, an advisor that became aware of an issue with the student should, where appropriate, pass that information on to the faculty teaching that student.


text:
Asking a company for permission to use website data for research
I'm a researcher, and I want to scrape a website (specifically, TripAdvisor) to collect data in order to use it for a research project. However, in reading the website's terms & conditions, I found that the company prohibits the user from:

...copy any content or information of this Website using any robot,
  spider, scraper or other automated means or any manual process for any
  purpose without our express written permission.
-- Prohibited activities, bullet (ii)

As such, I want to contact the company to ask for permission. I've had a difficult time finding any information on how to contact the company in order to ask for permission to use data. That said, my question is, when making these sorts of requests to companies, what is the best way to ensure that I am contacting the right department/person?

I foud only their physical mail adress. I need their e-mail.

Okay. I will leave this option as last alternative. Thank you

This is both too localized and not on topic. At best, you could edit to say "how to approach online aggregators to use their data for research", but I suspect that question would only have answers that don't help you ("find the email and email them"). FYI tripadvisor has a whole help center website where your efforts are probably better spent.

I have attempted to make the question more general, but it may need some additional tweaking (or it may not be a good fit for this site).

Ok. thanks all for your help. Very interesting.

You might also try to use LinkedIn a bit. If you can at least figure out the name of the department that sounds realistic for this type of request, you might have a better shot.

I always thought that the use of data could be beneficial for both parties.
By using Tripadvisor as benchmark Dataset, I think that the company will gain more visibilty in the field of scientists as a reference in benchmark dataset. And concerning the "Sounds realistic", I would say that I come here just to find help to get email, and not to covaince anyone to help me ;)

@Superbest - I've made a few edits to make the question more general. I think there's a good question to be asked here that's probably relevant to quite a few researching hoping to get data off public websites with similarly restrictive TOS.

@MOHBOB: "I foud only their physical mail adress. I need their e-mail." - well ... why? Why not simply send a letter (yes, on paper)? Deleting an e-mail is still a little bit easier to do than "erasing" a physical letter.

And, just for the sake of completeness, here is a forum thread on tripadvisor.com where another researcher wanted to get some data access in April 2016.

Thank you for your help @O.R.Mapper.
I live in a country where a letter to USA risk to take months to arrive. I wish if I could send simply a letter :)

@MOHBOB: Maybe that only applies to "normal" letters and there are priority services that can reduce that time to one or two weeks? Also, aren't there any web-based virtual-to-physical mail services that would let you upload a file online and then print it and send it physically from within the U.S.?

@O.R.Mapper:Thank you for your idea. Indeed it could be a solution. I'll think about it.

Firstly, recognize that they probably placed that ToS there for some or all of the following reasons:

They want a legal basis for suing someone who tries to steal stuff from their site.
They want a legal basis for suing some idiot programmer who brings down their site because of a poorly programmed bot he wrote "for a project".
Their lawyer told them to put these ToS up because he saw them on some other large site and thought they looked good there.
...?

You likely fall in the second category (and maybe the fourth, I don't know what other things they're protecting themselves from). To that extent, you have to convince them that you aren't an idiot who will run amok on their servers. If you're aligned with a well-known university then maybe you'll have more luck, but even then it'll be a stretch... this is a for-profit company, not a research institution. Even if you can convince them that you're not a total idiot, they still have very little reason to want to grant you this permission. Your pet project will gain them nothing, and may in fact demonstrate something bad about their site that they don't want public. The "I'll share my findings" argument really doesn't go very far... companies have their own interests, governed by many things, including politics, agendas, egos, and what have you. Your powerpoint presentation that may be done in a year or two that will probably be too technical for a business VP to understand anyways won't give them any business value.
The point of all the preceding words is just to convince you that you have quite the uphill battle here.
All that said, I would just start calling every "contact us" number I can get my hands on. Definitely start with the numbers on the "Contact Us" page. Don't be afraid to send a written letter! For phone calls, I like the phrase Jack St Claire used in his comment: "I have a weird question."
Success is easy to determine. Check your mail... do you have a letter (written or electronic) from the TripAdvisor legal team permitting you to perform the research? If no, then you haven't succeeded yet. Keep trying! Perseverance will be key here.

"but even then it'll be a stretch" - while your counter-arguments may be true in principle, I still think that statement sounds overly pessimistic. Research projects getting some temporary access to a company's data are by far not a rare occurrence ... or maybe that is my impression, given that I am from a field that is more likely to simplify usage of a company's services than reveal any undesirable details. In any case, my impression is that the companies' primary concern is less that a "pet project will gain them nothing" (that is somewhat compensated for by the simple fact that they'll ...

... get another little bit of publicity, (mostly) for free), but rather, that some of their data is not meant for public access (user data, paywalled data, ...), and that, once they have agreed to provide data, it can still be a bit of a struggle to actually get something moving.

That is exactly my opinion @O.R.Mapper.

@eykanal : I work on recommendation systems, and I see very often academic research projects using data from Tripadvisor.
For the argument "won't give them any business value.", it seems that Tripadvisor have the habit to give access to researchers, but request the findings as a counterparty.
I think that projects like recommender systems could be very beneficial for their type of service.

@MOHBOB - If TripAdvisor has a good reputation here, awesome! That's much to your advantage. From both my experience and that of my colleagues, most companies won't even bother to give you the time of day.

@O.R.Mapper - Having worked for now three of those companies, my experience is that (1) they are very conservative as to whom they share their data with, (2) they have a very dim view of academics, and (3) their impression is that any publicity you'll get them is just as likely to be bad as good. As such, they will be very unlikely to share data. Some companies will be different, of course, but that's my general experience.

@eykanal: Thank you for sharing your own experience with us. I think that a will use dataset from https://archive.ics.uci.edu/ml/datasets/ . I think that is more suitable for an academic project, and it's free (request citation only).

I would suggest 2 things.
1) contact other academic researchers who got this data previously (you mention in the comments this has happened) and ask how they did it. This is really your best bet and the only thing that has ever really worked for me.
2) Use LinkedIn to figure out who is likely to handle such a request. For TA it could be someone in their legal department or in their machine learning group, perhaps. You can at least get the sense here of what the departments are. I have used this method in the past to get responses to my requests, although they were "no".
Also I will note that I once had permission from a company to scrape data and then the company did not shut me down, my university did because it thought I was a "hacker from China". Then both legal departments got involved and took the data back. So try to get a dataset directly from the company, not permission to scrape.

I finally find help on ResearchGate.com. One researcher provided me some email addresses that he founds on this page and suggested that I email a request to the CEO (Steve Kaufer) asking for permission. I've emailed him a request, and I'm waiting his response. Hope this can help anyone in future.

Two comments: (1) The email address you posted is not necessarily correct (e.g., I found another one here... I suspect they're just following common email address formats), and (2) emailing the CEO of a $9B company asking for permission to perform a research study is almost certainly a dead end. The likelihood of your getting a positive response is practically zero.

Not trying to discourage you, but definitely trying to encourage paths that are more likely to be productive.

This is really not the person you want. You want someone like the head of research or the head of analytics.


text:
How to foster ideological pluralism in teaching?
It is common in Economics to have introductory courses based on one-sided ideological textbooks (e.g. the most famous being this one, ToC here). The problem of course is not the particular ideological orientation they have, but that most of these textbooks explicitly omit alternative ideological readings or understandings of the science. For example, the aforementioned book covers mainly neoclassical economics, and a bit of Keynesianism, amid a wide range of alternative schools of thought. The lack of acknowledgement of this wider picture nudge students to think that the science itself is defined on what the textbook presents. "This is Economics and nothing else".
Naturally, that is a deeply misleading view of a very diverse field, and particularly damaging (in my view) for those just starting to learn the subject.
Given this context, which are the best methods to foster pluralism in teaching, particularly introductory courses?

That is a very interesting question. I am sure there has to be a lot of experience on this in the philosophy departments out there.

@xLeitix Thanks. Regarding your last point, don't you think it provides some context upon which the question is relevant? In a sense, less effort is put on teaching because faculty is less interested, meaning the strategy required to foster pluralism might face extra complications than in a department which is primarily teaching-centered.

You appear to have very black and white views of your field, and of those in the field. That is your opinion, which is fine. But, you are projecting a great deal on others, so answering this question is ultimately very opinion-based.

Regarding your last point, don't you think it provides some context upon which the question is relevant? — Not without some evidence that disliking teaching is correlated with disliking pluralism.  Those dislikes look orthogonal to me.

There's a lot happening in your post (texts written with a particular bent, instructors set in their ideologies, teaching as a burden), but at the risk of settling on just one aspect of the question, you might consider contacting someone who has authored an introductory textbook, asking them why they made certain choices. If it's true that basic texts become popular because they are general and require less of instructors, then it is not unlikely that an author you contact may know of other, more "plural" texts, and can give you reasons why they did not take that route in their book.

@AaronBrick It is asking advice from a general perspective, without need to get into the details like a list of schools of thought to be taught. Taylored economic specific answers are surely welcome.

Erm... When I click on the "download" link in your reference, I just see some stupid set of three pictures instead of the book content. Can you post the link to the full text (and, if possible, refer to particular pages and passages) so that I could understand what exactly is the "ideological one-sidedness" you refer to before saying anything?

@fedja Added link to ToC. There is a wide variety of schools of thought in economics. The book covers mainly neoclassical economics, and a bit of keynesianism.

You need a Economics Science Educator Stack Exchange :-). Cf. https://cseducators.stackexchange.com/ and https://matheducators.stackexchange.com/

Tom Sowell's "A Conflict of Visions" takes an economist's point of view that might be helpful from a personal perspective, Robert Heilbroner's "Worldly Philosophers" give an interesting and fun tour of diverse economic philosophies. Exposure to others is the key.

How refreshing to see someone who recognizes a spectrum of ideas and wants to teach it!
Science in general and economics in particular could be said to revolve around observation of phenomena, theorizing about causes, and research to verify or falsify the theory.
Try addressing topics in this framework: Here's the phenomenon, here are some of the theories to explain it, and here is some research on it which supports / refutes particular theories.  This will provide a model for your students to learn the subject without descending into rote recitation of the professor's favorite dogma.

Ok, took a look at the preview. The key problem is, of course, that you cannot teach everything in one semester. The book starts in an absolutely correct way stating clearly what assumptions they make and what viewpoint they will explore in some reasonable depth. It is inevitable for any one-semester presentation even in such "uncontroversial" subjects as mathematics to be lopsided: you decide what highest points you want to achieve and essentially just combine the shortest routes to there allowing yourself some leeway for improvising occasional funny deviations when you feel like it. It is just the words "This is what the economics is about" instead of "this is the point of view that we will accept throughout this course to keep the exposition uniform and the conclusions consistent" that irritate one (especially if repeated more than once).
So, what I would suggest is to start with finding the depth-width compromise you want to make, to select sufficiently many points of views that you can explore in sufficient depth. Then, once you figured that out, choose the topics you want to present from these points of views and run some comparisons. That is a huge headache if you want to do it right and the goal is to give a clear picture of several approaches and their comparisons and interplay instead of just totally confusing the students so that the only thing they have in their head in the end is "everything is relative and you can come to any conclusion from any assumptions if you accept a convenient point of view" (I cannot really create such mess in mathematics, but I can easily make it if I ever give lectures on problem solving techniques, so I suspect your case is somewhere in between).
From what you said, it also looks like there will not be any single textbook you'll be able to use, so my advice would be just to lay all books aside and to plan the whole course without consulting any (I occasionally do it for graduate courses and for terminal undergraduate courses like "history of math" where I'm not bound by some particular curriculum requirements). Then you have two options.
The first one is just to declare a "no textbook course". The students usually squeak rather loudly when you do it (in the USA, at least; in Europe it is a more widespread practice) but if you have tenure, it shouldn't bother you too much. If you do it and you really care, you'll have to make at least some handouts emphasizing the main points, keep longer office hours, etc. I've done it several times with undergrads (I'm teaching math) and it worked more often than not, but it is again a headache.
The second one is to search for 2/3 textbooks and to assign all of them clearly stating in the syllabus what will be covered in each one and in what order. I have never done it (I hate to force the students to pay 3 times the usual price and I cannot legally just tell them to download everything from you-know-where) but it is still an option.
In any case, the point is that fostering pluralism in one course by one person comes at an enormous cost. If you are willing to pay it, by all means go ahead, but remember that the more traditional way of fostering it by spreading various points of view over different courses taught by different people works not too bad either ;-)

Excellent answer. I believe the "depth-width compromise" is the key here, and you treat it really clearly.

Thanks. You seems to focus specially on the issue of textbook (perhaps because I give that example). Are there other good ways to foster pluralism in a course? For example, debating?

@luchonacho Debating requires that the participants have some clear alternative points of view elaborated to a certain extent. If I tell you that the Earth is flat and rests on three elephants, you would know how to debate with me, but if I tell you that the the only way to get the $L^2$ boundedness of the Hilbert transform is by complex analysis techniques, I doubt you can debate this in a meaningful way (though, perhaps, I underestimate you :-)). Debating something without clear alternatives in mind is called "non-constructive criticism" and it is counterproductive more often than not, IMHO

@fedja yes, you are right, I don't understand why OP disregard science and already well established techniques in pedagogy

University Bayreuth offers a Bachelor-Master program in Philosophy & Economics. Their approach to economics is plural by choice. I haven't found any teaching material on their website, but most professors will be glad to share their experience when asked by a colleague. A list of staff can be found here: http://www.pe.uni-bayreuth.de/de/pe_team/index.html .

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


text:
How to get better at identifying research gaps?
One of the crucial skills of a scientist is to identify research gaps. Unfortunately, students rarely receive much formal training in this skill during their studies. How can one get better at identifying research gaps?

Some problems that I have seen which make identifying research gaps difficult:

The best problems are already identified or solved by other people.
Authors of publications sometimes avoid being overly critical of their own work, and try to phrase their publication so as to make it seem definitive, and avoid admitting that they failed to explain a phenomenon.
Some scientists are wary of being scooped, and avoid mentioning what they see as future projects in the discussion section.
Due to publish or perish culture, there is pressure to split research efforts into minimal chunks - such chunks may seem like they are steps along the way to a solution, but in reality, trying to work on the apparent next step is risky because the author is likely to scoop you.
High-profile journals such as Nature, Science or PNAS probably prefer papers which answer many questions, rather than presenting many uninvestigated open ends.
Lesser journals may have publications that have only solved part of a problem, but those may be buried under a sea of uninteresting publications. (also the lesser journals are much more numerous and harder to get abreast of)
It is easy to confirm that an idea has already been done, but it is difficult to confirm that an idea is truly novel.

What does a "research gap" mean to you?  Gaps in the body of knowledge of the field?  Gaps in one's own knowledge?  Gaps in proofs or other arguments? ...

@PeteL.Clark Questions which can be researched and published as an original publication.

I made a major revision to the question, which added some content that hopefully be useful to answerers. I am interested in feedback on whether this extra content should be altered or removed.

Join academic committees and attend their meetings. Most often, members discuss current issues "knowledge gaps" in their fields.

Finding good research "gaps" is indeed a challenging and important task. It has different components that all require slightly different skills.
Above all, a useful research gap is interesting, feasible, and unexplored:

interesting: I think this part goes without saying. But how do you determine 'interestingness' ? This is a complex mix of structural aspects of the field and community opinions, so it varies a lot from area to area. But probably the best way to understand what's interesting is by talking to people, asking them what they think is interesting, and why, and also understanding how even the basic questions in your field came to be deemed interesting (an advisor/senior researcher can often help with the latter).
feasible: It's not hard to list the "top 10 open questions" in your field. And for some researchers, that constitutes their entire research program. But that's not realistic for most people, and especially for students. Feasibility is about determining whether the tools exist to even make a dent on the problem. This requires a lot of experience in using different methods and understanding what they can and cannot do for you. It also involves thinking somewhat "sideways" about tools and problems, because it's likely that the obvious approach to an interesting problem has been tried. You will have to read papers very closely to find little gaps, or missing reasoning steps, that might suggest that a technique could get used. And you have to learn how to "fail quickly" when trying a new idea.
unexplored: While it might be educational to work on a new direction that has been explored before, you don't want that to be the fate of all your research explorations ! Here again, being plugged into your community and understanding what people have tried (or not) is also helpful. There are often "folklore" statements of the form "Oh this doesn't work because...". Sometimes it's true. and sometimes it's not. But it's best to understand what people have seen and what they're trying. Related to this is the idea of knowing your strengths: you'll accumulate a set of tools over time that you're an expert at. Make sure that you can use them: that gives you a competitive advantage.

We get a lot of questions here about whether anyone can do research (even if they're not in a formal academic environment). The answer of course is yes. But where amateurs (in the sense of people not being paid to do research) can often slip up is in identifying gaps that are feasible and unexplored (finding interesting gaps is usually not that difficult to do on your own) because they're not plugged into a larger commmunity.
Update: In response to the edit, here's an interview with John Baez that directly addresses the first point (of all the good problems being taken). John Baez's other suggestions are very good as well, and form a nice 'counter' to the Hamming article linked above.

I think you raise an insightful and useful point in contrasting with amateur researchers; I had not considered this (hence the +1). How do these three factors rank? Should I start by saying, "I have the following tools - let's see what problems I can apply them to"? Or should I find good problems and then look for the tools? When searching for an interesting, feasible, unexplored problem, in what order should I filter my search space? Find feasible problems, and see which ones are interesting? Find interesting problems, see which ones are unexplored?

@superbest: There's no one right answer. Any of these approaches can be successful.

What @NateEldredge said.

The only way I know is to read, read, and then read some more. The more you know and truly understand about your field and other fields, the better you'll be at identifying gaps. There is no shortcut to this. It takes a lot of hard work and experience.

Obviously identifying gaps in published research involves reading the published research. However, I find it hard to believe that reading indiscriminately is the most effective approach.

No one said to read aimlessly. You have to know about your field and you have to know about related / tangential ("other") fields. There is no other way to identify "gaps". As you develop knowledge about your research area, you'll develop intuition that will help you make intelligent guesses as to what may constitute interesting original research. It involves reading however. The only other way is to ask someone who has already done the reading.

I find that when lots of the other authors working on my topic area note what "future research" should address, it's a good indicator that there's some headway there. It's not a very good answer, but I am finding that the more I read and the better acquainted I get with the field and trends, the better I develop a sense of where there are "gaps".

Gaps could be a hindrance when creating a change in practice because there is no research to support the change or the use of an intervention. A thorough review of literature should be performed to identify validity and reliability before considering implementing a change in practice. A critical part of reviewing literature is identifying gaps, and when they are found an outline should show those areas of research that is incomplete. Sometimes gaps are a help if further research information can be found on the topic. So, there is a potential for further study or independent research. Also, a researcher can produce their own interpretation and suggest how future studies may carry on or what actions could be taken to fill those gaps to improve the topic outlook.


text:
Reference on availability of source code used in computer science research articles?
I have several questions related to open-sourcing the source code used for a research article.
Is there any research/study that addresses any of the following:

What percentage of research articles are provided with their source code? (i.e. the source code is made available somewhere online)
What percentage of research articles provide the source code at or before the publication date?
What percentage of research articles who promised they will release the source code actually do so?
What percentage of research articles provided the source code at some point but then the latter disappeared?

I am mostly interested in the field of computer science > machine learning, and English-speaking venues.

If you're looking for answers based on research/supported by citation rather than speculation and educated guesswork, please specify as much in the question, and add the [tag:reference-request] tag.

Certainly the algorithm should be published, if that's what's novel about your paper... but the implementation can be argued both ways. On the plus side, it means others can in theory check your code for errors. On the minus side, it means others may use your code without checking it for errors.

@ff524 Thanks for the suggestion! Yes survey/study/research would be much better than guesswork.

@FranckDernoncourt Great question! However, "how much time does it take to release the source code?" deserves a separate question thread.

@PiotrMigdal Sounds good I'll do it a bit later today (unless ff524's paper which I'll read in a few hours totally answers the question)!

@PiotrMigdal Done: http://academia.stackexchange.com/q/29233/452 Let me know if I need to change anything and feel free to edit.

@FranckDernoncourt Great! :)

While they are not answer, see also http://www.artifact-eval.org/ (also from the PL community) and http://reproducibleresearch.net/ (from closer to the machine-learning world).

Excellent question! I'm surprised that even in 2021 people are allowed to publish papers without original code/data.

@JonathanReez especially when funded by the taxpayers.

Here's a relevant study on computer science systems research that addresses your first question, "What percentage of research articles are provided with their source code?". The study is described in a tech report:

"Measuring Reproducibility in Computer Systems Research." Christian Collberg, Todd Proebsting, Gina Moraila, Akash Shankaran, Zuoming Shi, Alex M Warren. March 21, 2014.

The authors of this study observed the following protocol to determine code availability:

We downloaded 613 papers from the latest incarnations of eight ACM conferences (ASPLOS’12, CCS’12, OOPSLA’12, OSDI’12, PLDI’12, SIGMOD’12, SOSP’11, VLDB’12) and five journals (TACO’9, TISSEC’15, TOCS’30, TODS’37, TOPLAS’34), all with a practical orientation. For each paper we determined whether the published results appeared to be backed by source code or whether they were purely theoretical. Next, we examined each non-theoretical paper to see whether it contained a link to downloadable code. If not, we examined the authors’ websites, did a web search, examined popular code repositories such as github and sourceforge, to see if the relevant code could be found. In a final
  attempt, we emailed the authors of each paper for which code could not be found, asking them to direct us to the location of the source. In cases when code was eventually recovered, we also attempted to build and execute it. At this point we stopped — we did not go as far as to attempt
  to verify the correctness of the published results.

Here is a summary of their findings:

Total papers examined: 613
Papers that appeared to be backed by source code (not purely theoretical): 515

Of these 515 papers, 105 were excluded from consideration so that the resulting set of papers had no overlapping author lists. That leaves 410 papers, with results as follows:

Papers with link to source in the paper: 85
Papers not in above category, where source was found via web search: 65
Papers where author shared source following email request: 81
Papers where author declined to share source following email request: 149
Papers where author did not respond to email requests for source:  30

More details of methodology and results, as well as all the data and other materials used in this study, may be found at this web site.
There is an "Anecdotes" section appended to this tech report, which I think you may find very interesting, as it relates to some of the other points in your question. It documents the author's struggles to get authors to give up their source code :)

Thanks a lot! Brilliant study, lamentable results. I need to go shake my head for the next few months.

@FranckDernoncourt Re: the suggested edit, I deliberately did not copy images/tables from the TR in this answer because (ironically) I could not find licensing/copyright info for them

No pb, I wasn't sure either :/

From http://www.sciencemag.org/news/2018/02/missing-data-hinder-replication-artificial-intelligence-studies (mirror):

In a survey of 400 artificial intelligence papers presented at major conferences, just 6% included code for the papers' algorithms. Some 30% included test data, whereas 54% included pseudocode, a limited summary of an algorithm.

(Source: " At the AAAI meeting, Odd Erik Gundersen, a computer scientist at the Norwegian University of Science and Technology in Trondheim, reported the results of a survey of 400 algorithms presented in papers at two top AI conferences in the past few years.")


text:
Reference for annual journal subscription costs paid per university?
Is there any resource that lists how much each university pay in journal subscription fees? I am mostly interested in US universities (E.g. Harvard: $3.5M/year in 2014, MIT: $4M/year in 2006 for science and engineering journals alone), but still curious about other countries (e.g. French universities paid 172M EUR/5years to Elsevier, Finnish research organisations paid a total of 27 million euros in subscription fees in 2015).

By the way, the $3.5M figure from the Guardian is based on an very unclear Harvard memo, which stated that journals from "certain providers" cost Harvard nearly $3.75M in 2012 and that in 2010 the corresponding costs were 20% of the periodical subscription budget.  They didn't explain which providers those were, or what fraction of the periodical budget might be considered academic journals, so this leaves things rather uncertain.  But the total for journals at Harvard is almost certainly higher than $3.5M.

@AnonymousMathematician I totally agree, I was expecting over $10M/year.

Another thing that is unclear about Harvard's numbers is that they were most likely released as a leverage in a negotiation with large publishers. They preceded a bogus threat to 'suspend subscriptions'. I'm at Harvard and can access all journals from the big publishers via the library, and they most likely never had the serious intention to deprive their researchers from accessing the best journals.

Huh, looks like your $10M/year estimate was on target ($9,248,115 for Harvard in 2008, $16,391,638 in 2012).

MATLAB and NAG (two brands of computational software) also adopt this shady practice of negotiating their prices individually with the institutions and keeping them secret.

There is, in fact, a resource with the information you asked for, for institutions in the United States.
Detailed information on individual academic libraries' expenditures (by university) is available from the National Center for Education Statistics in the United States, as part of their Libraries Statistics Program.
The data from these surveys, including the individual responses from each university, are available for download in plaintext format at this link. The most recent year available is 2012.
To take your example, according to that data, Harvard's expenditures for library resources in 2008 included $9,248,115 for serial subscriptions. In 2012, this number was up to $16,391,638 (the most of any library in the survey).
If you're interested, a set of related information on amounts paid by selected public universities to specific major publishers can be found in

Bergstrom, Theodore C., et al. "Evaluating big deal journal bundles." Proceedings of the National Academy of Sciences 111.26 (2014): 9425-9430.

(see especially the supporting information for the latter.)

I know you're primarily interested in the US, but others reading the question title may be interested in other countries.  For the UK, see

Wiley/Springer/T&F/Sage/OUP/CUP (collected by Stuart Lawson and Ben Meghreblian)
Elsevier (collected by Tim Gowers)

For some information about New Zealand universities, see Mark Wilson's blog post and spreadsheet.

I don't know for sure whether there's a database that shows total journal spending at a fairly comprehensive list of universities, but I doubt there is.  There's not as much transparency around university budgets as one might hope (especially at private universities, but even at public universities).  [EDIT: As ff524 found, I was wrong about the existence of such a database.]
There is certainly no large-scale database that breaks down library budgets to show the amount spent for each publisher.  In fact, many bundle contracts explicitly keep this information secret.  Taking advantage of open records laws, Bergstrom, Courant, McAfee, and Williams managed to collect information about a number of contracts with public universities, leading to a paper and further information.  However, there are still many universities at which this data is officially confidential.

Some more data from https://ropengov.github.io/r/2016/06/10/FOI/:

Finland paid in total 131.1 million EUR subscription and other fees on scientific publishing in 2010-2015. The overall breakup of the
  costs is available as a separate table. The average annual costs for
  in Finland were 22 MEUR in 2010-2015; this is one third of the annual
  subscription costs in Austria (70 MEUR; Bauer et al., 2015), and
  two thirds of the annual expenditure (31 MEUR) in New Zealand.
  Data for the top-10 publishers in the UK 2010-2014 is available in
  Lawson, Meghreblian & Brook, 2015 (Table 1). During this period the
  UK paid altogether 4319 MEUR (rough estimate based on the exchange rate June 12, 2016) for the top-10 publishers. Finland paid 61 MEUR
  for the same top-10 publishers in the same period, which is roughly
  17% of the UK expenditure per capita (unexpectedly low?). The costs in
  the other countries seem unexpectedly high compared to Finland.

Some graphs from http://www.vsnu.nl/en_GB/cost-of-publication showing costs incurred by Finnish universities for books and journals by publisher:

FYI Why don't major research institutions systematically publish their subscription fees to scientific journals?


text:
Proving that the PhD work was done prior to someone else's patent
I'm in a peculiar situation, which I'll try to describe as concisely as possible.
Around three years ago I worked on something and I published a preliminary conference paper, which described the idea in great detail. I'm currently working on a PhD that's about this topic I published 3 years ago. Today I found out that there exists a patent that was accepted last year and it's like 50% about the same idea I published in that conference paper. Not 100%, it has some unique stuff in it and I'm pretty sure they didn't try to steal my idea, they probably came up with it on their own, that's why it has some additional features that I don't even need. But it's similar. I still haven't finished my PhD, but I'm worried—can this patent be a problem for me? I can prove with that conference paper that I was working on this idea years before the patent was submitted and published.
What would be the best course here? I was thinking of citing this patent in my PhD, but if nobody said anything about it until now, I'm worried I just might start opening too many questions.
Any kind of ideas are greatly appreciated. I'm really, really worried that my PhD thesis can become invalid because of this patent. Is that possible?

I feel like more information about how your work and the patent relate would be helpful, as well as the field. Is this a "I invented an algorithm and someone else patented a functionally equivalent algorithm"? Is this a "I had a physics idea and someone has patented a device that uses that idea"?

@Stella Biderman: I don't want to go into too much detail, for "security" reasons, but it's definitely the latter, although I later set up a similar "device" which overlaps with the one that was patented in about 50% or less. Although I was the first with the idea, the article proves that.

How, exactly, is this patent creating problems for you, again? You established the original idea with your conference paper and you're not the one trying to make money on that idea, right?

my PhD cite and use ideas from patents, I dont understand why is this an issue? you are aware that publishing and having a patent is different?

https://academia.stackexchange.com/users/41198/ssimon it's one thing to cite a patent and another to develop a similar device

You are right to be worried about a patent in the same field as your thesis research.
You do have some protection in the form of having "prior publication" that shows your work predates the thesis. But this is not necessarily sufficient to protect your future work.
I would get into immediate contact with your thesis advisor, as well as the legal department of your university. They are trained in handling such issues, and can advise you as how best to proceed so as to protect yourself.
Note that the goal of talking to the legal department is not to file a lawsuit. The goal is to understand what are your rights as a researcher working in an area with an existing patent, and how you can show that you are avoiding infringement.

The patent I'm talking about was posted by a large firm so I don't think anyone wants to involve lawyers here, especially not my department. I've talked to my mentor and he didn't seemed that concerned, considering the published articles I have in this field. I'm not exactly sure what you mean with "But this is not necessarily sufficient to protect your future work."?

It is public knowledge, with you having an early publication and them a filed patent (publicly visible), so I estimate it will not block off your publications (you need to cite them, though) and will become only a challenge when trying to commercialise. You can try to file for prior art if you are commercially interested - not fun, but that's how it is.

@WorriedAF See my edit above. You want to talk to a lawyer to know your rights, not file a lawsuit.

But this is not necessarily sufficient to protect your future work. -- If OP does not want to patent anything, I don't see how this even affects future work.

There is no reason to fear that your PhD thesis will be invalidated. It is entirely possible for independent work to happen simultaneously, and so long as your work is technically sound, the thesis and defence should not be affected.
However, looking ahead, if you want to further develop your device (assuming it is a device for simplicity), you may run into difficulties. If you are looking to monetise it somehow, you will certainly have a conflict with the patent and legal advice will be necessary. I believe this is what @aeismail meant with regard to future work.
While this may not be an immediate concern to you, I think the department would do well to look into it and protect it's IP if the idea has potential for further development, not necessarily commercial development alone. So while your PhD seems safe, you may still like to pursue these options because you may not want your work to be appropriated by someone else at a later stage.


text:
How should multiple Harvard references with same first author but different coauthors be made?
This question was written by a friend of mine. I'm helping them by posting it here, with permission.
How should I use the name-year referencing system (loosely speaking, the Harvard system) in such cases where there are multiple works that have the same first author but a different set of coauthors?
In such cases where the maximum number of authors among all articles sharing the same first author is not more than three, or perhaps four, the solution is very simple. Just mention them all inline and use the reference list as usual. E.g. the following:

"... the complex formation was observed by Miller and Nelson (1991)"
"... cf. Miller, Nelson and Byrne (1993)"

However, if there are more authors in any of the articles, this gets quite tricky, since listing a huge number of authors inline is definitely not an option to me. I'd rather change to number references.
Now, making the references unambiguous is not a problem. For instance, the following references could be addressed to inline as "Barton et al." without in any way losing the one-to-one relation between inline citations and reference list entries. That is, the articles are differentiated, as the other is "Barton et al. (1980)" and the other "Barton et al. (1985)".

Barton, D. H. R.; Crich, D.; Potier, P. (1985). "On the mechanism of the decarboxylative rearrangement of thiohydroxamic esters". Tetrahedron Lett. 26, 5943.
Barton, D. H. R.; Dowlatshahi, H. A.; Motherwell, W. B.; Villemin, D. V. (1980). "A New Radical Decarboxylation Reaction for the Conversion of Carboxylic Acids into Hydrocarbons". J. Chem. Soc. Chem. Commun., p. 732.

What really is the problem is the alphabetical order in which the references should be sorted in the reference list. If the articles listed above are referred to just as "Barton et al.", the reader does not know the exact position in the reference list where to find the articles.
One solution might be just ignoring this slight complication.
Other solution is to use "et al" in the reference list, too, if absolutely necessary. Thus, in the example above, the first article would be referred to as "Barton, Crich and Potier (1985)" inline, and the latter as "Barton et al. (1980)".
In the reference list, they would be expressed and arranged according to the inline cites:

Barton, D. H. R.; Crich, D.; Potier, P. (1985). "On the mechanism of the decarboxylative rearrangement of thiohydroxamic esters". Tetrahedron Lett. 26, 5943.
Barton, D. H. R. et al. (1980). "A New Radical Decarboxylation Reaction for the Conversion of Carboxylic Acids into Hydrocarbons". J. Chem. Soc. Chem. Commun., p. 732.

Any other recommendations?
Please don't suggest Google, since I did not find an answer after 30 minutes of search. There are perhaps hundreds of "Harvard citation guides" available, but I found none that addressed this problem.

This will typically be dictated on a journal-by-journal basis. As you suggested, some journals use first mention, some go alphabetically. It varies significantly by journal (e.g., Nature Neuroscience, seventh paragraph in linked section; IEEE (pdf), fourth page). Check with the specific journal of interest to see what their guidelines are for article submission.

Honestly, this is why I use a bibliography manager program. It saves you from having to worry about this sort of stuff.


text:
How to approach potential PhD advisors
What is the correct way for a new PhD student to approach an interested faculty member to discuss becoming their student?
Is it better to come with a few thesis project ideas prepared to pitch? Or is it better to come in expecting to have the faculty member to pitch them to the student?
Typically, the student has a year or two after joining a group to formulate an actual research proposal - but at the beginning of the program, when approaching potential advisers, there is only limited time, and limited knowledge of the lab's current focus and planned future projects.
Of course, the answer depends very much on the actual faculty member in question. But in what ways does it depend? Are there any aspects to the decision that remain invariant?
I am in the physical sciences (biology) but to make the question useful to more users, perhaps it may be better if we could have answers covering the peculiarities and commonalities of this question for different fields.

This will also depend on individual department cultures. For example, my grad department (Chemistry) ran a reverse lottery. Students had to meet with a number of faculty. Faculty generally tried to sell their research to the students (and not the other way around), who then ranked their top three choices. Faculty took every student who ranked them first if there was room in the group.

@BenNorris for my field (biology), it is common for students to do "rotations" to briefly work in a few labs, before deciding which one they like best. While often there are seminars where they present research to all students (to attract rotation students) I wasn't sure how it works after the rotation. Perhaps this would be a better question if I rewrote it to make the context of rotations more clear?

possible duplicate of Details an applicant should include/exclude in an introductory letter to a prospective grad school adviser?

(This is for Computer Science and Medical Informatics, I suspect that most STEM fields are similar.)

Is it better to come with a few thesis project ideas prepared to pitch? Or is it better to come in expecting to have the faculty member to pitch them to the student?

In my experience, if a faculty member is looking for a PhD student, they already have one or more projects in mind.
I think one reason for this is funding, and what faculty need to do to get it: The process of coming up with a grant proposal, submitting it, and getting a response takes months, and some grants can only be applied for once a year. That means that when you, the student, are joining the lab, there already is funding for you from a grant, and some general research goals are outlined in the grant proposal that your research needs to fall within. Some grants are more general than others, and there are also "training grants" out there the goal of which is to train you in a field (almost no constraints on the research topic).
The other reason is that faculty also have research interests.
I seriously doubt that you will need to pitch an idea out of the blue. It's possible that the faculty member will give you a general idea of what the direction of the research will be, since it would be under the constraints of their own interests and under the constraints of whatever grant is funding you, and then you would need to propose something more specific within those constraints. It's also possible that they will have something much more specific in mind and it will just be a matter of saying whether you're willing to do that research.

[A]t the beginning of the program, when approaching potential advisers, there is only limited time, and limited knowledge of the lab's current focus and planned future projects.

That's why you need to read up on the potential advisor's interests, look at their publications, look at the publications coming out of the lab, and figure out what the research focus and direction of the lab seems to be.

Thanks, although obviously one may question the wisdom of making a decision because "someone on the internet said so", I think you've answered my question by providing a clear argument phrased such that I can easily verify and reason about (especially the point about how grants tie in to the project selection process). I do of course try to perform my due diligence and understand their research, but you can only glean so much about their future plans from papers detailing what they have done in the past.