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Is it common for prestigious universities to contact you after you dropped out to see whether you wish to enroll again?
Many months ago, I had to drop out from a prestigious university.
Lately, the university contacted me and asked me if I were considering enrolling once again, and said that if yes, I should do so before a certain deadline.
Is it common for universities to contact drop outs?

"Have I left a good impression or are they interested in my money". Does it matter? You want (and afford) to take the degree or not?

You are right, but I haven't mentioned all the details (long story). My bad.

It depend somewhat on how many months is "many" - most institutions will give you a semester or two to get things sorted without officially dropping you completely from the program and requiring you re-apply.

You should be able to infer quite a bit from who sent the letter. If sent by the head of department in person, then they must care about you and your abilities. If sent by some admin outside of the department, then it's akin to the practice of banks to offer you credit cards whenever your credit has been good, in other words it's essentially computer-generated and the purpose is to get your fees (they know you're good enough since you were once accepted, so they are also saving the cost of interview, very rational practice).

@BrianDHall Really? I took two years away in the middle of my BA (one at another university) and had no problems returning for my final year. The transfer credits just needed to be figured out.

@PatrickT, The point is that I left in an angry way, and we were in a disagreement, and they made me feel like I was an irresponsible person (I underwent high pressure, and my future was on the line, plus my teammates had other priorities than studying, and team work was crucial). Consequently, the last thing I could expect from them is to give the chance to go back. An academic advisor himself told me "if you drop out, that means you'll never be part of the university again, right?", as think very carefully before you take such a "radical" decision.

@HalfLife, but did this advisor ask you to return? Anyway, think more about whether you want to go back and less about why they want you to go back, no?

The answer may depend on why you had to drop out, but many universities simply consider you to still be their student even if your studentship is disrupted by events beyond your control, and will assume you are likely to wish to continue your education there.
You do not say why you had to drop out, but common reasons for somebody to withdraw or fail include: mental health issues, financial crisis, physical illness, death or serious illness of a close family member, visa problems, etc.  None of these indicate anything negative about your potential as a student even if they caused you to fail all of your classes.  I have known people who dropped out for a wide variety of such reasons, many of whom then returned to finish at the same prestigious institution after their life circumstances had improved.
Many universities thus make it easy for a student who left for such circumstances to return and complete their studies, and that is likely what is going on with your university as well.

Many students who drop out eventually return, and being away from the university they may be unaware of the deadline. So they may have simply been sending a courtesy message informing such people of when the deadline for re-enrollment is. There probably isn't any deeper meaning than that.

In theory the classes you took should be good forever, and the program would never change.  If this were strictly true, then you could take classes for years, a few at a time and with frequent long breaks and still obtain your degree.
Most schools consider students to be students from admission onwards, and they never take them out of the system.
However, degree programs change, requirements change, and the schools must change their curriculum.  While they grandfather in older, possibly out of date classes, and older programs, they have to limit them, and the easiest way is by time.
If you start a bachelor's program you can expect to be able to follow it without issue for 4-6 years without change even if the program changes for newer incoming students.  If you change degrees you'll have to adopt a new program.
However, if you drop out of school, the school doesn't think of you as a person who will never return.  But if the programs and classes are changing they will remind you, even if you haven't attended for some time, that in order to fit under the old program you'll have to complete it by a certain date.
So this is why they've sent you a letter.  You are, in their eyes, still a student, eligible for a degree in a specific program, and they want you to be aware that even though you haven't been in some time, if you had intended to complete your education with the program you started then you will have to do so by a deadline.
Not all schools send out such letters.

Watch out for phishing; they may not be who they say they are. Don't give the caller/writer any information beyond what you'd give to a stranger on the street, and if you choose to give the issue further thought, verify the offer at the admissions department's public phone number.


text:
If I appeal an admission decision by a German university at the court, would the department take it personally?
I've applied to a graduate program at a university in Germany and there is relatively clear evidence indicating that they've missed one or even two of my documents in application review based on the responses they've given me. Now they are reluctant to reconsidering my application when I resent the documents to them and explained how those documents mean the reason they mentioned for rejection is clearly not true. This is not a subjective thing and it's completely objective and bureaucratic.
It's stated on my rejection letter that I could appeal the decision at the court and I have their emails where they explained reasons that are in contradiction with each other about those documents, which could help me make the case. I really like that department and want to have the option to go there later in my academic career, but I'm afraid if I take my complaint to the court, the department may develop some level of animosity towards me.
Do you think I should forget about working in that department if I start an appeal process at the court, or could I assume that everyone could just be adults and behave professionally?
Note that while I asked previously about what possible decisions to take, this is just about the consequences of an appeal at court when it comes to working with the department in the future.

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Perhaps you can explain what you mean by 'bureaucratic and objective', because the current phrasing makes it doubtful whether it is really such a clear-cut formality. For example, did the uni tell you they didn't consider you because you didn't supply a translation of some certificate, although you did?

@henning They told me that I don't have the required minimum number of ETCS in my undergrad degree, while I actually have more than what they said is required. They explained the reason for rejection to be that I've had fewer major courses that I actually had (in fact around one-third of what I actually had). The reason for confusion seems to be not counting the courses that were transferred into my degree from where I transferred to the institution I graduated from.

It's just a university.
I wouldn't bother in going to court just to enter a specific college. You're taking it more seriously than you should, for there is no university that should be considered with that attitude. Remember there are many more out there.

This depends on a lot of factors:

Who was involved in the decision to reject your application and replying to your inquiries?
Only these people (plus their superiors, such as the head of the admission committee or similar) have to be involved in taking this to court and know of it.
However, to what extent you can rely on only these people being involved depends on administrative legislation, which probably only a specialised lawyer¹ could tell you about.
If your application was rejected due to lacking strict formal requirements, this was probably done by administrative staff, and you are strictly speaking only “attacking” them.
If on the other hand, your application was rejected after an interview process or by a committee involving scientific staff (i.e., usually professors), the situation is different.
Is the application handled by the university, faculty, or the department?
(You can usually find out by looking at whom you interacted with so far.)
Now why would this be important?
In Germany, there is usually a certain animosity between departments and university-level administration.
Scientific staff usually won’t care much if their university’s administration is attacked because they are used to them botching things, but they can get protective of their own department’s administration, who may be much more valuable to them.
How valid is your claim? Your case will be viewed differently if somebody really botched something during the process than if all you have in your favour is a technicality.
Did you exhaust all other options? Even if you have been clearly been wronged, directly escalating to court instead of trying other methods of resolution will not be in your favour.
What happens if you succeed? The best you can expect in most cases that the admission process is resumed at the stage where you were rejected.
For example, if your application gets rejected on the entrance check, you still would have to go through an interview process.
Unless you and the university want to wait for the next regular round of applications, this means you get an extracurricular interview, etc.
Now, if everything goes really professional, all those participating this application will only learn that your application has to be re-evaluated due to a clerical error.
But you have to ask yourself how likely this really is depending on the above.
Are the positions limited? Would you be taking somebody else’s place? There are master’s programs where everybody with a suitable bachelor degree will be admitted, and the crucial selection is who gets a scholarship (because most students need one). In this case, suing for admission is more likely to be seen as an administrative issue (which the academic staff doesn’t care much about).

At the end of the day, a lot can happen between the full range of:

Only a few people you will never interact with again know that you went to court.
Everybody knows that you are the person who sued themselves into the programme due to a technicality and nobody will accept you into their group (for a master’s thesis) since you are presumed trouble. On top, everybody hates you because you are the reason that the admission process was overbureaucratised the next year.

¹ whom you should probably consult anyway

Brilliant response, +1. The outcome analysis is particularly helpful.

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What to do when I think a published paper displays academic misconduct?
In a paper published recently in a math journal, the main result is presented as being new, but in fact it is not new, and I'm sure that the authors knew this before submitting the paper.  I have informed the journal editor who handled this paper, who told me he would forward my message to the managing editor.  I have not heard anything since then.  What else can (or should) I do?
For what it's worth, I am a tenured professor.
In more detail, there was a previous paper [A] which proved a certain result (1).  The proof given in [A] actually proves a stronger result (2) which has a messy statement, and notes that (2) implies (1) (where (1) has a simple statement).  The main result (3) of the recent paper [B] implies (1), but is implied by (2).  Moreover, the proof in [B] is identical to the proof in [A] (and the authors of [B] say this in their paper), except that the proof in [B] uses a stronger auxiliary result at one step.  So the authors of [B] must have been aware of the stronger result (2) proved in [A], but they do not mention (2) in their paper, and certainly do not mention that their main result follows immediately from (2).  To me, this shows that the authors of [B] published their paper under false pretenses, by intentionally misrepresenting prior work.  In addition, the auxiliary result mentioned above is presented as a new result in [B], even though it has been published several times and also the authors of [B] were fully aware of this fact, since they had written previous papers citing an essentially identical result from a paper [C].  Even beyond this, the paper [C] contains a result which is stronger than (1), (2), or (3), although the authors of [B] do not mention this.
If people think I am overreacting, I would be happy to hear this.  It's possible that my views of proper academic behavior are not standard ones.  I don't have a fully articulated philosophy about these things, I just feel like the authors did something wrong and should not benefit from doing it.
Added later: The situation has been resolved.  The journal's editor informed me that, after inspecting the documentation I sent him, he has decided to require the authors to withdraw their paper from the journal.  I don't know the logistics of this, but to me it seems like the appropriate outcome.

It might be wise to consider contacting the authors before fetching your torch and pitchfork. Maybe they didn't do these things with bad motives as is portrayed here.

I worry that if I contact the authors, and if I'm right about these things, then I might receive a mailbomb as a reward.  Seriously.  That's also the reason I posted the question anonymously.

@user14857 Not every mathematician is a Ted Kaczynski. :P

But what good will come of emailing the authors?  Of course they'll say they didn't do anything wrong. And even if they don't actually kill me, both they and their friends would despise me, which can cause me trouble I don't need.  I don't see this as me-vs-them, I see it as the facts-vs-them.  So I just want to put the facts in the hands of the right people, and then have this be handled by the appropriate mechanism.  But I'm not sure what that mechanism is.

The way in which they say that didn't do anything wrong can be telling; for example, do they claim they didn't read the earlier papers that included their result? Do they claim they read them but forgot about them? Or do they dispute your claim that their results are the same as the earlier ones? etc. In case there is some reasonable explanation, arguably the proper course of action is to give the authors a chance to present it first.

Also, I think it's a good idea to keep any concerns of non-academic retaliation (i.e. any talk of mailbombing and murdering) out of this question. It seems you have some reason to believe these particular authors are highly unstable, but for other people who find themselves in a similar situation (of having found possible misconduct), that will not be the case.

Let me congratulate you for seeing a publication practice that you suspect is fishy and taking the trouble to inquire about it.  This is something that contemporary academia really needs: we are self-policing, so when we let these things slide it is as though we are sitting back and watching a robbery take place from the comfort of our squad car.
Here are my reactions to your story.

You make a very compelling argument that the authors of [B] should have known better than to try to publish their paper.  The details you provided do not yet compel me to believe that the authors did so deliberately or with malicious intent.  Math papers are hard to read: just because you cite one theorem from a paper does not necessarily mean that you are aware of the other theorems in the paper (you "should be", whatever that means, but that's not the same thing at all) and just because you come across an equivalent version of a theorem does not necessarily mean that you see that it's equivalent.  Rather recently I got sent a draft of a paper that contained three theorems.  They looked interesting, so I read more deeply.  It turned out that two of the three theorems were not new.  How did I find that out?  By reading the papers cited in the bibliography!  But one of the papers was written in a manner where it was a little puzzle to decode every single result (and the author did not shy away from stating more general theorems with more complicated statements; I can't argue with that, but it certainly does make the paper harder to read).  The point of the story is that the people who sent me this paper were not bozos: the third result was very nice, and I have just written a paper with them that builds on it.  Or here is an even more personal example: in my PhD thesis I combined work of Ogg with more recent work (of Ribet and others) in order to determine whether certain Shimura curves had points over Q_p.  I didn't write these results up right away, and when I looked back at them a couple of years later I had to reread the paper of Ogg to refresh myself on what he had done.  I was surprised to see that one of the theorems from my thesis was already proven in Ogg's paper!  My proof was not the same as Ogg's, but neither was it "better" in any clear way.  This may not be that different from what you're describing.  These things do happen.
Divining the authors' true motivations does not seem to be your job as a self-deputized academic policeman (if it is, you have an awfully hard job).  What matters is that a paper got published that doesn't do anything new and that in fact cites the paper that majorizes it.  That's bad no matter what the authors were thinking...but when you look at it that way, doesn't a lot of the blame rest with the journal's handling of the paper?  It seems like a referee who was a true expert in the literature or honest and conscientious enough to track down the citation should certainly have caught this issue and prevented the publication of the paper.  The journal looks bad just as the authors do.  If they are really not being responsive to this, they look even worse.

It seems more likely that the journal is looking into this but doing so slowly (this involves a lot of delicate conversations, including with the authors of the paper), and in the meantime they are not doing a good job of assuring you that they are actually doing something.  You say that the matter got referred to the managing editor.  If you have waited what you think is a reasonable amount of time and not gotten any further response, by all means take it up directly with the managing editor.  It would be pretty surprising if you didn't get at least an acknowledgment of the issue from him/her within a few days.  If you really hear nothing back, then waiting a week or so and sending a followup email conveying the fact that a total lack of response is only going to make you have to do more yourself to deal with the situation seems in order.
That "more" would involve talking publicly about the situation: e.g. bringing it up to other mathematicians you know and, depending upon the importance, raising the issue on a site like MathOverflow, putting something about this on your own webpage, writing a letter to the editor to some other journal, and so forth.
Finally, let me say that proper police work here may require giving up your anonymity.  I think you should be willing to do so if it comes to that.  In your comment you say that you are "[s]eriously" worried about getting a mailbomb from the authors.  Seriously seriously?  You think that some ethically questionable mathematicians are likely to commit a violent felony??  I find that hard to believe, but if it's really true you need to contact the actual police.

Wow.  Thanks so much for the encouraging and insightful response!  I feel a bit like I'm following in Serge Lang's footsteps, by not being silent when something seems wrong.  But I've heard many mathematicians suggest that although Serge was usually in the right, he often took things too far and caused bigger problems than the issues warranted.  So I'm nervous about whether I'm doing the right thing.  Regarding this case: the authors of [B] had to know result (2) from [A], since result (2) is the next-to-last assertion in the proof of (1), which they basically copied as their proof of (3).

Lang did sometimes take things too far.  Probably part of his motivation for doing so was that many people do not take things far enough.  I agree that moderating your own level of involvement is a good idea.  If it were me then I would certainly follow up with the managing editor of the journal, more than once if need be.  If I didn't get any response at all I would consider calling them.  I would probably not do much more than this unless the paper was playing an important role in someone's career.

Regarding your followup information: okay, it sounds bad.  I agree that if you are convinced that the authors behaved unethically, then it seems pointless to contact them directly.  Contacting the editors will (at any rate should, and you can check up on this) get them contacted indirectly anyway.

@PeteL.Clark I've been enjoying catching up on some of your answers here on academia.SE, but I disagree with this one. Though it is 10 years old, it seems to me that the OP was overly sure that something unethical has occurred, almost certainly didn't have the full story, and I would NOT advise them to "go public" till they were much more certain, with real evidence to back it up. It has happened to me several times in the past few years that some young scholar posted a paper to arxiv that proved a theorem that was a special case of a theorem I had already proven. Instead of insisting that...

...they not publish, I have instead encouraged them to still publish their paper, because they need that publication to have any hope of getting a job, and to simply add a line like "White has also discovered this result." I encourage them to emphasize the application they had in mind, and any differences between their proof and mine. To an outsider, it might look like they "should have known" that the result was known previously, but new researchers often don't. I think there should be space for a bit of duplication as long as it falls short of outright plagiarism, and as long as their...

...paper still has other positives making it publishable. In most cases, I don't think the field is served by random observers aggressively asserting ethical breaches when they just don't know for sure, especially if the authors are junior. Also, big schisms, hot heads, and public brawls don't serve us either. It's often better to let things lie and let emotions cool. I say this as someone who has 100% for sure been scooped by someone else, and I have emails to prove it, but I never "went public" or tried to trash their career. And that person went on to do some good work so I'm glad I didn't.

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To enroll in to a PhD Program at the age of 65
As a retired school teacher, and to become a professor at a university. Is it okay to get into a PhD program at the age of 65 and complete it to become a professor? Or is it too late and I can’t get employed at a university?

Anecdotal evidence: we have two above 60 PhD students here. Yes, possible. I doubt that they are planning to become professors though.

I wonder why you want to become a professor after 65? If you give your reasons, some may be able to provide more relevant answers. For example, if you have a big idea that you want to investigate and give to the world, then, big-ideas have not just come from professors. Gödel's outstanding contribution was (partly) before his PhD, for example.

Agreed with @ThomasKing - your goals here are very important.  Do you want the PhD in order to work on original research, do you want it so that you can teach in higher education, or all of the above plus a hope that you yourself will also be able to supervise new PhD students?  Would the field be in a field related to your existing expertise (subjects you teach already and know well) or would it be a break into a new field?

I think we need to know which country you are living in. I am aware of more than one country where Ph.D. students are employed by the government, hence subject to mandatory retirement restrictions.

I second the comment of @CarlChristian. For example in Germany you would already be too old to become a professor. There are laws that define that. "Just" getting your PhD on the other hand would be possible without problems if you find an adivsor.

I think this is three questions: 1. can I get my PhD  2. can I get into a PhD program and 3. can I continue to work as a professor.
I'm planning to do just 1. I'm doing the research on my own, then I'm sure I can find a professor and work with them for a year or so and get my PhD. Here in the Netherlands, 2 would be hard, 3. would be impossible unless you're Albert Einstein.

See also https://academia.stackexchange.com/questions/3426/how-old-is-too-old-for-a-phd

Possible duplicate of How old is too old for a PhD?

The realistic answer is: you can enroll in a PhD program at age 65. However, you are highly unlikely to get a tenure-track professorship after finishing a PhD program at that age. The big reason for this is that you're already above the retirement age, and many schools do have rules about how old you can be and still advise students. Moreover, you probably wouldn't represent a good "long-term investment."
On the other hand, you may be able to obtain a position as a part-time lecturer or adjunct faculty—in other words, for positions where you are not directly supervising PhD candidates.

At least in the US, it is generally illegal to discriminate based on age. Do you know how that works in a situation like this? I agree a tenure track position would be tricky though!

Most states are also right to work so employers can fire or not hire for any opinion they come up with after the fact as long as they don't say it to your face. I've actually had a cease and desist letter sent to an employer spewing garbage after the fact. Needless to say he forbade anyone from saying anything less risk a lawsuit but that may be as far as you can go.

@chessofnerd: I think the big issue would be is how competitive a 70-year-old's profile will be versus a younger person's, especially if the younger person has a postdoc under her belt, and the elder person only had a doctoral degree. It wouldn't be an "apples-to-apples" comparison, so age discrimination wouldn't be the deciding factor.

You can only prove age discrimination if they are stupid enough to tell you that is the reason. Just because the 28 year old got hired and not the 65 year old isn't proof of age discrimination.

@MaxW That's super true. I tend to agree a 65 year old is almost certainly going to have a hard time at this. I wish them luck though (if not for job prospect, for personal enrichment)!

Thanks for all the valuable replies....the reason of this typical question is as follows:

Well let me explain my career...I worked in Indian Army...for 24 yrs retired at 46...then  did my MS, MBA worked in corp ..became a guest professor at Univs in India...enrolled in PhD in India, completed recently. I had moved to USA in 2003 on GC........after coming here applied at Univs for a faculty job ..but they were not hiring... so I got certified to teach in schools...but I was never satisfied with school teaching. I could not get faculty job. Now I thought probably if I do 2nd PhD from US it may give me a chance to teach at higher level and also earn. Not looking for many yrs to work..

Thanks for all the valuable replies though...I do not mind relocating if anyone has any suggestions about applying to a particular University...

@Neil: Why not work as an adjunct lecturer?

@chessofnerd As I understand US employment law, you can discriminate if there is a factor of the job that would make that requirement important (for example, you could refuse to hire a male OBGYN if the clinic was for abused females who were afraid of men). If the University could come up with a suitable reason not to hire a 65-year old person (for example, the tenure-track would take to long) then they would likely be able to. It's why Hooters are allowed to hire only female waitstaff, as it's part the business identity.

I have a friend who started a PhD in late 50's and is planning to become a lecturer.

@chessofnerd In England and Wales it is illegal to discriminate on age, except you can refuse to hire people above retirement age.  Are you sure there isn't a similar exclusion in the US?

" many schools do have rules about how old you can be and still advise students." Can you please point to a few examples of established rules at some schools regarding this?

I don't have the links handy—however, faculty in several departments in the US told me that, and I know for sure in Germany that the only way to continue to advise students after 65 is with the blessing of the successor. (In other words, if the replacement faculty wants to take over everything, you're out of luck!)

@AdamDavis at my uni if you are above 60 you are not allowed to be the main advisor.

@MartinBonner: Having a mandatory retirement age is itself illegal in the US.

It could be hard to get into a PhD program since potential advisers will be looking for students who will have many productive years ahead to establish a legacy.  But you don't need a PhD to be a lecturer at most universities here in the US.  You only need a master's.  It's not the same as the tenure track positions, which actually have professor titles, but the students still call you professor.
I'm 66.  I fell into teaching when my department chairman at University of Washington Bothell posted a request onto an IEEE email list for industry veterans to advise teams of seniors on their Capstone projects.  I thought I was volunteering to do it free and was surprised it paid and even more surprised they'd pay me.  With only a master's, it was never on my radar that any university would let me do this.  At Washington, I was an affiliate (part-time), but that led to being recruited to a full-time three year appointment at University of Michigan.  It's possible it could happen to you, too.

can you finish phd?

I studied in computer science.  We had two older instructors without PhDs who came in retired from the industry.  They were paid dirt but they were already living off retirement and passionate about helping the students.  As far as I know they were part-time.

@SSimon  I never started one and at this point, I think that ship has sailed.  When I first started teaching at UWB four years ago and realized a career in academia was something I really wanted, I applied to the PhD program on our Seattle campus but was not accepted.  It's possible they decided I simply wasn't that good or that while I was a good candidate for teaching, that I wasn't that promising for research.  (No one tells you why you weren't accepted.)  But I also suspect the limited number of productive years I could offer past the PhD was a factor.

@NicoleHamilton can you apply for grants and reaserch funding without phd?

@SSimon  Yes, it's possible but you won't be supervising PhD candidates and, realistically, you may not have time for research given your service obligations and the heavier teaching load you'll have as a lecturer.

@Pace  Yes, the big downsides to an affiliate appointment are that the pay is less than for a full-time appointment (even with the same teaching load) and you may not get benefits or an office or the right to vote on faculty business.

@NicoleHamilton In Germany, you would have much more rights, since now having experts teaching and supervising is a huge trend. I suggest you to try

In most academic fields in the US it takes most people 10 years or more to go from the start of a Ph.D. program to starting a tenure-track academic position.  This includes the time to get a Ph.D. plus one or two postdoctoral or visiting assistant professorship positions.  If you start at 65 you're going to be looking for permanent positions when you're 75, and odds are that means you'd be looking at 10 years of preparation for a position you're likely to hold for less than five years.  You would also probably need to move to a new city at least twice during those ten years.  That doesn't seem like a great plan from your point of view.  Also it's not clear at this point whether you will still be interested in and able to do the job in your late 70s.  Lots of people at your current age are effective faculty, but the vast majority choose to retire before their late 70s.

How is what the "vast majority" of people do relevant? The OP specifically asked whether it would be possible to get an academic job after completing a PhD. Even if the OP only does hold a TT job for five years, maybe that would be five very happy and productive years, fifteen if you count the PhD and postdoc. And no one ever knows how much longer they have. Why is it still socially acceptable to devalue someone because of when they were born?

I’m just suggesting the OP think about the timing.  Maybe he will want to keep working in his late seventies, but the odds suggest that’s not the most likely scenario.  Might be true for him, I certainly have great colleagues in their late 70s.

This may be difficult for younger academicians to comprehend: There is the adage that 'Those who can, do; those who can't, teach'. Let's say that I earn a B.S. or M.A. in computer engineering and go onto to start my own company, make a gazillion dollars, sell that company and start another. I sell that company and now have a net worth of twenty billion dollars. I'm sixty years old, I have the time and money. I've made my fortune, set up a foundation to do good works, and am now eager to explore other areas of life. I think, why not get that PhD? It has nothing to do with teaching; it's about challenge, accomplishment, and completion. And who knows, maybe some university will hire me--not because I'm young, but because I have wisdom and life experience.

And if you can't teach, teach the teachers, if that fails, become on inspector...

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text:
What is the best technique to represent similarily among different methods?
Lets say I have 3 different methods. I am trying to find the best technique to represent similarities (or differences) among these methods.
One way I thought of is to create a table and create my own correlation methodology (e.g., high, medium, and low). However, I am not sure if this is the best way to do it.

Here is the corresponding LaTeX code I created (just in case):
\documentclass{article}
\usepackage{booktabs}

\begin{document}
\begin{table}
    \centering
\begin{tabular}{llll}
    \toprule
             & Method 1 & Method 2 & Method 3 \\
    Method 1 & High & High  & Low \\
    Method 2 & Medium & Low & Low \\
    Method 3 & Low & Low  & Low \\
    \bottomrule
\end{tabular}
\caption{Level of correlation among different methods}
\end{table}
\end{document}

Is it mathematics? Do the high and lows represent some numbers?

No not necessarily. It is general methods, for example methods to clean the house method 1 (vacuum) method 2 (broom) etc. And the similarity (high medium low) represents similarity.

In that sense, many factor will come into account. Time, Energy, Man Power, Cost etc etc... So these things should also be reflected in your representation.... By the way, do you have taken all these into account and accordingly saying High, low or medium...?

For simplicity, I assumed that my correlation methodology of high, medium, and low could represent an average representation of these metrics. My issue is my way of representing it is the best or their could be other, I was reading about heatmaps but I don't know if it could be the way.

I assume that the high, low and medium corresponds to some analytical values and are dependent on various factors. So how about to assign some values to all constraints and so to this high, low and mediums also. Then finally show as an shaded matrix plot e.g.,

Thank! what tool did you use to create this ?

You can do it in Matlab, or GNU Plot or GIS ... Here is an example of GNU Plot and that to for heatmaps also http://gnuplot.sourceforge.net/demo/heatmaps.html

I suggest that you put characterizing features in the rows or columns of your table. For the descriptions, you can put simple explanation to the advantage or drawback of the $feature_i$ in $method_j$. Something like, faster timer, or heavy memory usage. It depends on the field.


text:
Should I present future research directions in a separate section while writing a scientific paper?
Should I present future research directions in a separate section while writing a scientific paper? Or to mention it in its related section?

Anything is Okay. I have seen the future directions in both ways: mostly I found it in the related section, however it is rare in a separate section. So choice is yours. But keep one thing in mind. Your future direction should not be too long unless your presenting results and discussion are enough to be accepted by the reviewers. Otherwise, reviewers of your paper may feel the future directed works are important part in your present paper and may give a comment like "why didn't you conduct same work for this paper?"

In most of the good papers I have read, the directions for future work are typically mentioned in the conclusion and/or a discussion section (if it exists), and sometimes partially in the related work section if relevant.
The conclusion section is quite apt for this because you can closely link it with a summary of your main proposal and/or results.
I think it largely depends on individual author(s') choice, you general organization of the paper, and also on the type of paper you are writing.
Is it a survey paper (of the state of the art) or a paper detailing your novel contributions? In the former case, it may often be prudent to have sections or sub-sections under each section (e.g., if there's a section per theme you survey the SOTA for). In the latter case, it is typically done as part of Conclusions; some elements of the future directions may also appear in a separate Discussion section (if any) that critically analyzes the core contributions you've made in the paper until that point.

You can discuss future directions in related work if related work section comes at the end of article i-e, just before the conclusion section. If the future work discussion is long, then I recommend adding a separate section before conclusion section; otherwise, discussing it within the conclusion section will be better choice.


text:
How to review a software-tool paper?
I often get asked to review papers on new software tools. This always makes me wonder how one should review such a paper, or even whether software papers should undergo a typical review process at all?
My private checklist typically consists of:

Is it available for download for others?
Does it run?
Did the authors provide benchmark problems? Do they give expected results?
Is documentation sufficient?
Go through numerical methods used in the software (briefly, no meticulous code analysis)

If everything runs fine and produces expected results, I honestly have nothing else to “demand” from the authors. My referee reports are positive and (embarrassingly) brief in those cases. I’m of the opinion that the user community should “do the rest”; evaluate the software and decide whether it’s useful in their workflows.

I'm also asking myself, whether the software improve user experience or user dealing with the target domain compared to current tools? How much does the software facilitate the target domain for non-experts?

I think this must be field dependent, since I have published several tool papers and my papers would fail your checklist.

The problem I have is that even tools that pass this checklist when being published often fail point 1,2 or 4 after two updates and one year passed.

One perspective is from the Journal of Open Source Software, which explicitly establishes reviewer guidelines that cover these questions (http://joss.theoj.org/about#reviewer_guidelines).
A (slightly edited) quote of the demands:

Software license
  There should be an OSI approved license included in the repository.[...]
Documentation
  There should be sufficient documentation for you, the reviewer to understand the core functionality of the software under review.
A statement of need
  The authors should clearly state what problems the software is designed to solve and who the target audience is.
Installation instructions
  There should be a clearly-stated list of dependencies. Ideally these should be  handled with an automated package management solution.

Good: A package management file such as a Gemfile or package.json or > equivalent
     OK: A list of dependencies to install
     Bad (not acceptable): Reliance on other software not listed by the authors

Example usage
  The authors should include examples of how to use the software (ideally to solve real-world analysis problems).
API documentation
  Reviewers should check that the software API is documented to a suitable level. This decision is left largely to the discretion of the reviewer and their experience of evaluating the software. [...]
Tests
  Authors are strongly encouraged to include an automated test suite covering the core functionality of their software.

Good: An automated test suite hooked up to an external service such as Travis-CI or similar
     OK: Documented manual steps that can be followed to check the expected functionality of the software (e.g. a sample input file to assert behaviour)
     Bad (not acceptable): No way for you the reviewer to check whether the software works

Community guidelines
  There should be clear guidelines for third-parties wishing to: Contribute to the software, report issues or problems with the software, or seek support

This is a valuable way of thinking about reviewing software, and I think we should move closer to this. But it is not yet accepted! In my field, most "methods" papers don't even include software - and those that do would almost certainly fail these tests. (I'd never heard of continuous integration until recently, for instance.)

I have never reviewed an article but as someone that produces software (in bioinformatics) this is what I would like to know from a reviewer, expanding from your list:

Is it downloadable and has a license?
I modified your first point because the code should be available for others and should have a license to known what other users/developers can do with that tool.

Does it work well? Do the authors made an effort to write the best tool?

Could you install the tool in your settings?

Are my tests enough to check that the software work as expected?

What else could I do to ensure that it works well?

Is the language of the tool a good choice?
Is there a community of users and developers for that niche in that language?

Is it under version control? Is the tool under versioning?

The tools are usually developed when there is a problem:

Does my tool solve correctly the problem targeted?
Could this tool be used in other problems/situations I haven't thought of?
Are there other methods to address the problem I am not aware of?
Did I take into account all the relevant factors or I forgot something?

The tools are usually tested in a given dataset or compared to different tools as noted in a comment. This can be interesting if negative results are reported too.

Did I choose a good dataset ?
Did I choose well the tools to compare my tool with?
Is documentation sufficient?
How easy is to understand how does the tool work?
Does it clearly explain when you should use this tool?
Does it provide enough examples or scenarios where this tool could be useful?
Are the functions/methods/modules... easily understandable?
Do I need to explain something better?

The software sometimes is developed by several people and several years:

Is the tool documentation consistent? Did I forget to make the style and documentation coherent?
Does it have a clear focus? Or did I went off at a tangent with other functions that don't bring anything to the tool and/or problem?

When using the software questions will come, you as a reviewer can check how will be handled:

Does it have support from the authors? In a mailing list, a forum or alike? Preferably open to avoid having two users to have the same question
Is the long term support explained or thought?

As you noted some of these question might be addressed by the community but you as a reviewer have the opportunity to check that the article of that software explains and solve a problem for the community, that it is reasonable well done and well thought.

I have only written but not reviewed such a paper yet. My personal perspective comes from the fields of complex systems and scientific computing, but I offer some generalisable ideas.
I structure my answer by the typical criteria applied to research papers:
Soundness
This is arguably the most difficult-to-translate and most field-dependent aspect.
For example, in a simulational or experimental field, it is not feasible to completely verify the results of a research paper, as this would mean completely redoing it from scratch – all you can do (and are asked to do as a reviewer) is to check whether the employed methods are appropriate and the results are consistent.
On the other hand, in some theoretical fields, you can (and are expected to) check every calculation and proof.
I suggest to apply the same standard to software papers than to research papers and in particular method papers in the respective field.
After all, if a software paper gets accepted, it should be citable as “evidence” like a regular research paper and in particular, a methods paper:
With other words, citing the software paper should suffice as evidence that the respective task was done properly¹.
So, as a practical criterion:

Consider a typical paper that would cite this software paper. Assume that the paper satisfies you with respect to scientific soundness otherwise.
Suppose that the citation would be replaced with the content of the software paper.
Would you still consider the paper scientifically sound (according to the standards of your field)?

More specific criteria would include:

Are the employed algorithms, libraries, etc. appropriately chosen, i.e., can they be hold to the same standard, do they fit the application, and are they state of the art?
Does the paper sufficiently back up claims made on the correctness, efficiency, and usability of the software? This point may slightly differ depending on the format of publication. For example, if the software itself is regarded as part of the publication: Can you verify these claims (possibly using provided tests, benchmarks, documentation, and examples)?
Does the software sufficiently adhere to good software-engineering practices such as tests that ensure that it works as intended?

¹ barring the correct handling of the software, which should of course be appropriately described by the citing paper

Novelty
If the venue of publication has a novelty threshold, try to translate it to software.
Pragmatically, you ask yourself whether the paper in question will contribute positively to the journal’s impact factor (or some other metric).
Some specific criteria that come to mind:

Can the new software perform any tasks that have not been automatised before?
Is the software more efficient, more accurate, or easier to use than existing softwares by a relevant factor?
Is the software a module for a programming language that did not have such a module before and that is relevant for scientists in the respective area²?
How likely would you consider it that a user of an existing software performing the same tasks will switch to the software presented in the paper?
Is the software sustainable, i.e.: Do you expect that the authors or somebody else will maintain the code in the years to come? Is the codebase maintainable and extendable or was it legacy code at the moment it was written? Does the software depend on some exotic libraries that may break in the near future³?

² Who would need a CAS library for Malboge?
³ This is an actual problem: One of my motivations to write a software for a specific task was that existing softwares either depended on discontinued and deprecated libraries or on a library that was heavily changed in a non-backwards-compatible way (which in turn was possible because hardly anybody used it).

Other Criteria
Most other criteria should be easy to translate, in particular when you think of a method paper:

Is the paper well written, using a reasonable structure, consistent terminology, and so on?
Is it clear for which tasks the software can and cannot be applied?
Are any shortcomings of the software (efficiency, scalability, problems with specific tasks) properly discussed?
Are possible future expansions and improvements properly discussed?

Many thanks for the bounty. I am surprised to get a bounty (I can only see the "Draw attention"  on the history of the question). May I know why I was awarded the bounty (considering you have an answer here)?

@Llopis: I set a bounty to draw more attention to this question, in particular to attract voters for the answers, given that the question has considerably more votes than any of the answers. As I cannot award the bounty to myself, I awarded it to the other answer which I considered best, which happened to be yours.

The actual answer mainly depend on the specific journal/conference/workshop. My own experience is from High Performance Computing - there may be some field-dependent common practices, but I think most of it will be similar.
The main thing I see differently is that you are not reviewing the tool, you are reviewing the paper. Also a paper about a tool is not the same as  documentation. Focus your review more on the scientific contribution of the paper rather than the tool itself. Ideally the paper itself should be useful without the tool. I would even argue that a paper describing a failed attempt of developing a new tool can be a valuable contribution for a slightly restricted audience.
There is no general limitation to open source tools (unless of course your venue is the Journal of Open Source Software). At least for HPC, paper about proprietary tools are not uncommon. However, publicly available tools do improve the reproducibility of a paper.
At the same time, any scientific paper should include a proper discussion of related work. The paper should describe tools that use similar techniques or address similar goals and how the new tool is different. If the tool leverages a published technique, it should be referenced. The related work can also include references that underline use cases.
A tool-paper doesn't need to produce an detailed description on how to use the tool, but should focus on the novel concepts applied in the tool, be it in terms of implementation aspects or features. Use cases are also an important part, but more with a focus to evaluate the tool (e.g. performance comparisons), and how it is useful rather than instructing the user how to use it.
While some workshops have a clear focus on tools, there are not only pure tools papers. It is possible to present a tool for X-analysis/optimization on a workshop on X. Or if a tool makes heavy use of a technique from Y, it would fit for a Y-conference. This shift in audience should reflect in the focus of the paper.


text:
Would it be safe to assume that TA and tutor are the same thing?
I am currently an Australian studying at ANU. I have worked as a tutor for about a year and now I am about to apply for a Ph.D. program in the states. Since the US uses TA (teaching assistant) instead of tutor (at least my institution uses this term.) When listing my teaching experience, shall I use TA or tutor as a title? Are they the same thing?  I run labs or tutorials, I mark exams and assignments and so on.)

In my experience (at a US school), "tutor" usually refers to someone who gives one-on-one instruction.  Usually this is not part of the course itself, but is something that students who need help seek out independently (that is not to say that the school or department might not have some program for tutoring, but it's usually not considered "part of the course").
In contrast, a TA is someone who does grading, leads review sessions, helps proctor exams, or some other activity related directly to the course.  A TA often also has office hours for one-on-one help, but this is not their only duty.

In the U.S. and for math, graduate student TA's can also teach classes entirely on their own, but this is usually not until their 2nd or 3rd year, after the graduate student has had some reasonably successful experience as a TA leading recitation sections. Sometimes a graduate TA will begin teaching classes their first semester of graduate study if the graduate student has some prior teaching experience.

I would not change the job title. List it as tutor and then provide a brief description of your job duties. In the US a TA can have duties ranging from only grading problem sets to independently running a class. When evaluating an application the admissions committee wants to know what you did and not what your title was.


text:
Can I resubmit the article?
I submitted my revised paper (second-time major revision) just few days back through Scholar One. Now I found some errors in my submitted paper. As the paper is already submitted, what shall I do? Can I write a mail to the editor-in-chief?

Depends upon the specific journal's policy and system. Have you contacted them? I doubt anyone here can help you.

Generally, you can’t change the submission once it’s gone through.
If the errors are truly minor (typos and grammar errors), then it’s not worth it to go through the trouble of alerting the editor. Just correct the problem before the next stage.
If it’s a material error (including the wrong version of a figure, for example), then you should alert the editor and ask for guidance.

You can email the editor or the handling editor about the error you made in the submission and it's important to include your Manuscript # or code so they can easily track it. I experienced before I mistakenly uploaded a different cover letter for a different manus. I emailed and explained the case what they did was reopened the system so I can modify my submission, however, the "Date Submitted" has changed.


text:
Why are not more sophisticated algorithms used to handle the fake paper problem of the science?
Talking a lot about people in the academic world, I experienced a general unsatisfiedness of the customs of how the funding agencies (mostly, governmental entities) measure the scientific results. Their general view is that the stats are easy to trick, a large part of the science world is doing that, and that makes most of the publications wrong.
Also various trick were explained, like if "friend" departments cite regularly each other in various publications and so on.
For example, if some U.S. federal ministry decides, how to divide up R&D budget in the next year. I believe, the decision makers doing there the hard job, decide about not little sums and probably not anyone can get into there. Also their obvious goal is to do the best for the science (of the U.S.).
How can it happen that they do not use a better stat? Considering the importance of the budget to divide, I believe there should be human resources available to invent stats which can not be tricked even by scientists, particularly if even the details of the algorithm are not public.
(Related material, partially to show "basic research")

How big is science’s fake-paper problem?

I believe every worthwhile stat can be tricked.  The people devising the tricks are just as smart if not smarter than the people devising the stats.

This seems like more of a rant than an answerable question.

@Buffy Absolutely not! All the people with whom I have talked until now, without a single exception, said roughly the summary of this question. I am really sorry if it looks ranting, but to my best knowledge, I am explaining the common opinion of the academical sphere and not a rant, but a real problem.

@AlexanderWoo 1) That looks right, but committing all possible would be likely better than doing nothing 2) It is not a big problem if the rules can be tricked. Everything can be tricked. The achievable goal is to make the tricking harder than doing real science.

@peterh - My belief is that the difficulty of tricking the rules is always going to be about the same as the difficulty of implementing the rules.  So rules that are harder to trick than doing real science will also be harder to implement than doing real science - do you want scientists spending as much time to evaluate the work of other scientists as they spend actually doing science?

@AlexanderWoo As far I know, evaluation happens by processing openly available publication metadata with open and simple algorithms. I can not see a major obstacle before hardening these algorithms against trickery.

As a suggestion to improve your "question", consider looking through US funding agencies to see how they state they evaluate research proposals. Then, cite these in your question.

@RichardErickson I can not. Very likely, I would not even understand it. I am fully out of this world. This is why I asked you. Without any ranting intent. I clearly feel that you don't really like this question, but I do not understand, why. Would you check the veritasium video (first link in the post)?

Proposals are evaluated on a very clear matrix by a panel of other scientists. Not sure where you are getting the idea that citation rates play a big role beyond pointing out that one’s previous research was well received and impactful

What even is a "fake paper"? That "most published research is wrong" does not imply that anyone has mis-applied statistics or is trying to "trick" people, it's more a result of the types of experiments that are done to show effects of unknown size, and the publication biases of reporting those results. There is nothing inherently "wrong" with most of those papers that can be identified from the data or analysis itself.

@peterh - I believe every algorithm that comes from processing openly available publication metadata is easily trickable (in the strong sense that someone could come up with an algorithm that takes as input an evaluation algorithm and gives as output an easy way to trick it).

@peterh I am encouraging you to follow this site's recommendations for asking a "good question". If you cannot be bothered to do basic research, why should people be bothered to help you answer your question?

@RichardErickson I believe, the content of the two links in my question qualify as basic research. Could you please detail, how my post would not qualify your link? Did you check the links (particularly the first one)?

@AlexanderWoo Ok, but actually re-wiring hardcore science work in order that the algorithms show a false result, that might be harder. For example, to selecting pals on tricky ways for creating cooperative articles (or refering each other in publications).

@Nuclear How big is science’s fake-paper problem?

@peterh The answer suggested in that link is "not very big" - it suggests that "fake papers" are at least an order of magnitude less common (~1%) than legitimate papers whose results cannot be reproduced (>10%).

@peterh YouTube isn't academic research, especially when primary sources are easy to find with a search engine. For example, the US NSF lists their funding criteria on their page. Nowhere do they mention the statistics you're talking about.

@RichardErickson Here the "most basic research" criteria clearly does not mean academical research, but a reasonable initial investigation of the topic. More details can you understand by reading (possibly asking) on this meta site or on https://meta.stackexchange.com . Note, also the nsf.gov link you are pointing to, contains a youtube video. Did you read the links in the post? It would be important to get a context.

@RichardErickson I think the topic is actually far not so flaming as the question title might suggest. If the title is the problem, I would happily change it to a better one, but I have no idea, to what.

I don't believe there is an objective, quantitative/algorithmic way to solve this problem. The systems for "gaming" that you refer to exist because those things are used as quantitative measures. It's a far bigger problem in systems that have used algorithmic solutions entirely to make hiring/grant giving decisions.
The alternative is to bring in more subjective evaluation, to let experts decide what the value of some scientific proposal or accomplishment is. The problem with that is that subjective evaluations are...subjective. They suffer from bias or appearance of bias. Sometimes forces outside science demand a more quantifiable approach because they fear abuse otherwise.
In the US most grant agencies and universities/hiring committees use a combination of these methods, not either in isolation.

+1. However, it's not only "forces outside science" that push for more objective criteria, it is certainly also people within academia who fear that subjective criteria give too much influence to "old boys' networks", and I am using the term "boys" advisedly. It is not the case that there is a "good" solution here that is only suppressed by sinister forces with an agenda.

Yes indeed; I didn't mean to imply only outside forces have that influence, rather that sometimes the decisions to use those tools and even which to use are not up to academics themselves.

There are two misconceptions in your question:

You think that the fact that there are no better ways to detect fake papers is because nobody has cared enough to develop them. But that's certainly not true, many very smart people have looked at this problem, but found that it is just very difficult to automatically detect whether a paper is "fake" or not. The problem is that a paper is just several pages of text, and to detect issues with natural language text is just difficult all around.

At a deeper level, it is difficult to detect "fake papers" if you have trouble defining what exactly a fake paper is. These papers are not just a random collection of words, but they are written by humans, oftentimes on topics for which they have made experiments or calculations, that are shown in the papers. To a non-expert, they will look exactly like any other scientific paper. To an expert, they will (i) show results from experiments that are unsuitable to illustrate a specific issue, (ii) use inappropriate statistics, (iii) are on topics that are simply not of interest to anyone. But these "fake papers" are generally not complete fabrications, showing figures with data completely made up, machine-generated text, etc. -- most of these papers took actual work to write, though perhaps less work than writing legitimate papers.


text:
My paper was rejected following a lengthy delay during which an editor published a similar paper
I have had a very bad experience with a journal. After nine months under review, the system showed that a decision had been made; I have checked and was “revise and resubmit”. Two days later, the editor contacted me to let me know that the paper has been rejected.
I don’t how to proceed with that journal and felt really disappointed and frustrated especially after it took such long time to respond. I also discovered that one member of the journal's editorial board has published a similar paper in the following issue.
Any advice on how to handle such a situation?

Did you get any reviews together with the decision? Was the decision, based on these reviews (if any) justifiable?

Did you have an pre-print version on arxiv?

i did not receive any reviews... the editor have decided that it does not fit with the scope of the paper

Nine months without a review is unreasonable. You may want to consider contacting the publisher or editor-in-chief.

I would understand nine months with constant revisions and feedback but nine months for the first bit of feedback, which is reject, is totally unreasonable whichever the journal.

You can mitigate against being scooped by releasing technical reports prior to or after submission.

thanks a lot for your comments and answers, I appreciate your feedback. unfortunately, i came to realisation that some journals, even highly ranked in my domain, use some unethical manner for publishing articles. have you even experienced that? i wish if the process is much transparent as it takes a lot of effort and time to do research and make an article ready for publication.

Do you know when the paper from the editor was submitted and accepted?

I would suggest submitting your paper to a different journal, but as a counter to the charge that "it's already published in journal X," include the correspondence you had with journal X.
This should alert a responsible editor to the fact that something wasn't right at the other journal, and may be willing to give your paper a fair shake.
I'd also consider lodging a complaint with the publisher of the journal. This sounds like an ethical lapse somewhere: another paper got published, but yours was out of scope?

Thank you for your response. I think the same; there is a clear issue with the ethics of this journal and I would like to warn other researchers about that instead of loosing such precious time without even having feedback on my submission.

I disagree with the first part of your answer. If you submit the paper to another journal, they would be justified to say that they do not publish articles as proof of priority but to communicate knowledge. No matter how justified your claims are, the scientific value of a second publication would be zero.

@Jan-ChristophSchlage-Puchta: The paper is described as "similar," not "the same." There may still be value if the work differs in some important way.

I think it's best not to assume the worst, since there's a good chance what happened is the unscientific nature of the peer-review process manifesting itself. For example, it's conceivable that the two papers were handled by different members of the editorial board who were not acting in consultation, and one felt the topic was out of scope while the other didn't.
Taking 9 months to decide a paper is out of scope is terrible. However it's also conceivable that they received some confidential (or very poor quality) reviews that they can't share and think the best thing to do is say that your paper is out of scope. This would explain why the decision was "revise and resubmit" for a brief time. There's no way of knowing unfortunately.
What to do now:
1) Next time, if a paper goes more than a month with no sign of review, I suggest emailing the journal office and ask for a status update. It's possible the paper got lost in the system, or simply wasn't submitted correctly. One month should be enough for the journal office to say something, e.g. "we've invited three reviewers of which one has agreed to review, the review is due in 16 days".
2) You can lodge a complaint to either the publisher or the editor-in-chief. It depends on who the editor that rejected your paper is. If that editor is an employee of the publisher, then I would complain to the publisher. Be sure to emphasize that taking 9 months is unreasonable. If it's a member of the editorial board, then I'd approach the EiC, since the publisher is likely to defer to the EiC. If it's the EiC, then there's no point complaining.
3) Submit the paper to another journal. I wouldn't tell them that the paper was rejected at the first journal, unless they ask. You gain nothing by doing so, but could trigger subconscious biases ("we have no idea what to do with this paper, but since the other journal rejected this paper I'll agree with their editor").
4) If you've been scooped, my first inclination would be to complain to the employer of the editor who scooped you, but I genuinely don't know if that's a good idea.

I agree with this.  It could be plagiarism, but it could be coincidence, and plagiarism is hard to prove when it's about an idea rather than identical text.

For biomedical authors - PLOS Biology publishes complementary research. If you have been scooped, you have six months from the publication or posting (to a preprint server) of the first article to submit your manuscript to PLOS Biology. They hope to tackle the science reproducibility problem with this approach. You can see more details about their new policy in this article.


text:
Recommendation from institutional email or private?
I recently went to a summer program. Now, I’m asking my mentor there for a recommendation for college. The email account she uses for all correspondences related to the program is private (Gmail). The institution she works at is not related to the summer program in any way. Now, the college asks for the letter to be sent through institutional email accounts (letters from private accounts will be subject to further review).
She wouldn’t be sending the letter in her capacity as professor at the college she works at, but rather as mentor in the program, an institution in itself.
So should I ask her to send it through her private or institutional email account?

You seem to have answered your own question. If you don't want the recommendation to be subjected to further review, you should ask her to use her institutional email address. Anyone can set up a Gmail account, whereas there is a level of authenticity implied by an institutional email address. It's not relevant that she isn't sending the letter in her capacity as a professor, since the main purpose of the email address is to authenticate who she is. The college are requesting that letters of recommendation are sent from institutional email addresses since it reduces the amount of extra work required of them and of the recommender.

She wouldn’t be sending the letter in her capacity as professor at the college she works at, but rather as mentor in the program, an institution in itself.
Nope, wrong.  The way she knows you is through the summer program, but her authority to speak about what would make you successful in college is based on her position as a professor.  That's a key part of what makes her letter credible (beyond the confirmations that it's literally her who wrote it). Writing such letters is part of the job of being a professor; the email she uses should reflect that.


text:
How detrimental is a large lab cohort to a graduate students’ success?
A PI I might potentially apply to is planning on making three or so offers. Said PI only has a few students at present which I think is the reason for their doing so.
I worry that I will not get my hands on very many projects and will not have enough time with the PI. So my question is: How detrimental is a large lab cohort to a graduate students’ success?
I think it is important to mention that this is a social-sciences PhD program with cohorts of around ten or fewer. This situation seems unique as the PI needs students this year. Most labs only take one student per year.

It depends a lot on how things are set up, what the culture in the "place" is. If students work effectively as a team, this can be advantageous and better than having a single student who is left alone with a research topic.

Related, but not necessarily a duplicate, given that it is about a field with potentially very different group dynamics: How many students are typical for an advisor?


text:
Are arXiv papers more read than the journal versions?
I have a conference paper which is published at IEEE with some errors unfortunately. But I have submitted a version on ArXiv without the errors.
As a researcher, I honestly prefer reading versions on ArXiv because I always think that if such an error has been detected by the authors in the official version (i.e., IEEE, Springer, etc.), they will of course have tried to correct it in their ArXiv version. That is why I usually prefer to read ArXiv versions or that ones present on the authors’ personal page.
Some researchers told me that papers on ArXiv (or HAL for example) are more read than the official versions. Is this true?

Are you in math (or in a different field where practically everybody puts the paper into arxiv)?

Are you just curious about this, or is there an action item behind it?

Hello @Buffy the action item behind my question is that I want to know if most of researchers will make attention to my corrections on arXiv rather than just reading the official IEEE version that contains errors.

Most researchers aren't interested in any given paper. The few who are will go where they like. Your actions to produce a correct version are good, but you can't control what others do. Better to be more proactive before first publication. At this point, it is what it is and it can't be other than it is.

The field should be specified in the question as this will vary greatly by paper topic.

A suggestion: if you do make any changes to the arXiv version after publication, make note of the differences in the arXiv document itself and in the arXiv's comments field for the paper (and also on your web page where you link to the paper) so that people can find out which version is more correct.  (Many people will otherwise assume that the published version is more correct/final, since many authors fail to update their arXiv preprints when making revisions based on referees' comments.)

@AnonymousPhysicist It is mathematics.

Well, statistically speaking, ArXiv requires no reader subscription, so more people have access to it (regardless of what publications they or their institute pays for). Ergo publications on ArXiv have the potential receive views from a wider audience. Whether this translates to citations or not is another argument.
It’s relatively common in my field to see an author "park" some research on ArXiv before submitting it to official publications or conferences. The publication process can take a while (and conferences have fixed dates), but the paper might as well gather interest and citations during that time.
I’ve never heard of anyone publishing on ArXiv after publishing in a journal, but I have seen post-conference extended papers (which go into more detail without the page limit). I don’t know what copyright you signed over (or what access level your publications have) when you published but I’d be wary about infringing the official publisher's copyright by posting on ArXiv.
———————-Edit———————
Well, according to comments, some journals explicitly allow publishing to ArXiv (or related sites) after publication. That might depend on gold access level, but it makes sense for journals to make ArXiv an ally rather than an enemy. Relevant xkcd.

Thank you for your answer. I have submitted to arXiv before my official publication. But when I saw my paper on IEEE, I detected some errors, and so I went directly and updated my arXiv version. So I want to know if most of researchers will make attention to my corrections on arXiv rather than just reading the official IEEE version that contains errors.

I have published on arxiv after publishing in a journal - but my field is chemistry (on arxiv stat.ML) and [some] chemistry journals may make a fuss about previous publication if the manuscript is already on arxiv. Whereas the copyright transfer explicitly allowed me to put the authors' accepted manuscript to arxiv.

"I’ve never heard of anyone publishing on ArXiv after publishing in a journal" I always do it that way.

The first paragraph was confusing: it started "Well, statistically speaking" but then described an argument based on intuition, not statistics. Statistically speaking would be if there were some statistics available about how often people read arXiv and journals.


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Can I write publications if I don't have co-authors?
I'm currently studying a BSc so I'm not fully involved in academia yet. I'd still like to write some publications and have them peer-reviewed about specific subjects.
According to Does one need to be affiliated with a university to publish papers?, I can publish even without an affiliation, but do I need co-authors? If so, how to find any?

Yes it definitely can be done.
If you have an idea then do a literature review of the subject and if you have a contribution that builds on the activity in one of the journals you find then publish there. Perhaps also look into doing a conference paper first. See here for the difference between the two.
The best co-author for your case would probably be a professor or grad student at your university.
No, co-authors are not required. They can be useful though if you need their help/skills in the project.
In computer science, journal papers usually occur during one’s PhD. Bright Masters and Honours students usually start publishing conference papers, but journal papers are not unheard of.

Note that there are fields in which conference papers basically don’t exist.

@Wrzlprmft As far as I understand Luca is a CS guy and there many important papers are submitted to conferences.

@Alexandros: But the question has not been asked specifically about the field of computer science. So if a part of the answer is specific to this (which is fine), this should be marked. As it is written right now, this is a wrong statement – though the intended statement is correct.


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I am afraid of being stuck in the administrative/teaching side of the academia in my country
Disclaimer After I have read the title, I have understood that it might be misleading. I do not mean that being a teaching staff or administrative staff is somewhere to be stuck with. For starters, I want to be involved in the academia as a scientist, and scientists are not so much valued in my country.
I am at a point in my life that I am too much concerned for my future. In fact, this is the only time period that I have that much concerns.
I seek for any advice that can take me out of my downward spiral.
My job conditions

I am 26 years old.
I have finished my master's last year.
I have a full-time job in a university since November 2011.
I am also a PhD student in that university since February 2015.
Even though my job title is "research assistant", I do teaching for 8-10 hours a week and exam proctoring for 6-8 hours a week on the average.
Because of my teaching duty, I prepare quizzes/assignments and grade them as well, which approximately takes up to 5-6 hours per week.
Sometimes, I have extra administrative duties that might take up a full day or so.
It has been one year after I've finished my master's and yet I have no publications.
My thesis adviser also suffers from the administrative duties and has little to no time to carry out research with me.
There are no research groups where I work. Even though there are some people those want to carry out group studies, they are either too busy or their areas of interest are different than mine.

My personal issues

Despite the question I have asked before, now I do realize that I really enjoy research. By research, I am not talking about the fun parts, but struggling with seemingly most boring and useless parts.
I usually study for long hours as a block to be productive. For instance, if I start studying at 10PM, I finish at 3AM or so. However, my productivity drops when I divide my working hours into multiple periods.
My job does not let me study for a long time continuously.
I do not want to, and more importantly, am not capable of working in the industry.
I feel like I am inside a downward spiral; such that more time I spend without publications, the harder I gain scientific reputation around the world.
Since my life-goal is to be a scientist, I need to find a paid PhD position in a country that values scientists to be happy with my life and do my part to prepare a better future for my soon-to-be spouse.
When I do not gain enough reputation around the world, I probably will not be in the shortlists of the universities.
I do not have enough experience to carry out a research all by myself. Even if I do, it will probably end up as a trash.

Conclusion

I have no hard proof that I am able to do research other than some first attempt technical reports and my supervisor's reference. Hence, I am naturally being turned down by most of the universities since I have no proof that I can do research.
I am afraid of being stuck in the country that I live in, and being a person that has no other choice than work as a full time college member full of administrative duties and no research practice.
If I finish my PhD in my current university, the above situation will be inevitable for me since I probably will have no publications and the same process will follow me through post-doc applications.
I have limited funds.

Miscellaneous Points

I have applied to a PhD position requiring a considerably low fee and have agreed with my potential supervisor on principle. However, that university requires some sort of paperwork to recognize my master's diploma. There is a chance that I don't obtain a recognition and miss the deadline for enrollment.
Most of the universities with paid PhD positions either require publications or reference from their own faculty members. Unfortunately, I have neither of them.

My choices that I have thought of so far

Applying for master's positions with scholarships and start all over again.
Quitting my job, dropping off of my PhD and ask for internships from various research groups across Europe, hoping to find a job. By doing this, I would be risking all my savings and coming back to where I start with nothing.
Applying for industry jobs, and submit applications to PhD positions without scholarships after I save some money.
Accepting the fact that I was born unlucky, and carry on with my life with below-the-average happiness.

More on the country that I live in

It does not have a good reputation throughout the world.
In most of the universities, your publications are only "something that you do for yourself". As long as what you do does not attract potential students, the university prefers you to work harder for your administrative duties.
Even if you are capable of invent teleportation, and obviously so close inventing it the administrators will not appreciate this unless you do your job.

Are you referring to institution that is on your profile? Before doing anything from your choices, you should publish more papers, one thing is for sure, you need to change your working environment, since it is not what you expected,

Applying for master's positions with scholarships and start all over again.
You wrote in [previous question][1] posted by you, that you dont like taking exams and classes, is this situation changed now? Why you dont apply for PhD position with scholarship? You need to know that you cannot be professor with master degree,
Quitting my job, dropping off of my PhD and ask for internships fro...e,
you need research experience for that and EU passport, otherwise you have exchange schemes and other programs that help in institutional cooperation of EU and your country, have you heard about it?

I thought I'm the only one who has similar dilemma in this stack exchange.. seems like you have it more difficult than me.

I disagree with you that applying for a masters's program is like having to "start all over again."
In the US, it isn't unusual to have two master's. I know many people who got a master's from one school and then another from their PhD school.
Also, Research Assistants have very little obligations other than fulfilling their [small] course requirements. Again, this might be different in other countries but is typical in the US. You may be expected to be a Teaching Assistant prior to becoming a Research Assistant but it will be a lighter work load than what you have now.
Taking this route is what I would expect from anyone who isn't coming from a top-tier university, so go for it!

"Again, this might be different in other countries but is typical in the US." - indeed, especially the existence of a strict distinction between research assistants and teaching assistants, and any assumptions on what spectrum of tasks these jobs imply vary wildly between countries.

@O.R.Mapper Right, and the OP made a few comments that make it clear  they are looking to move to a new country to improve their circumstances in this manner. The US provides that, for the little info we have about the OP's situation.

Concentrate on your research. If the Powers That Be consider you too valuable as a researcher, you might get away with little administrative responsibilities. But being a successful reserarcher means you'll end up managing your graduate students, research group, ... In a sense, it is inevitable. Best you can do is to avoid too boring tasks...

Unfortunately, as a research assistant, one is as valuable as he/she carries out the administrative duties as much as possible. I probably might not get away with little work


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Can I upload a modified version of a code from a journal paper to Github?
I am new to Github and I want to upload some scripts that I developed during my research. One of the scripts requires the use of a small external program (not mine) whose source code is included as supplemental material in a journal paper. Can I upload the program and/or the source code of that program?
The journal is Computers & Geosciences.

The answer to your question depends entirely on the license of the "small external program (not yours)".  Where did it come from?  Find its source and read the terms of the license.
If it's an open source license or a free software license, usually you are permitted to redistribute it so long as you preserve attribution and license terms in the code header.  If it's a different type of license, then it will depend entirely on the content of the license, which acts like a contract between the author and yourself.
UPDATE w/ JOURNAL SPECIFIC DETAILS:
The Journal of Computers & Geosciences is published by Elsevier who has an open access publishing option for authors.  If the paper in question was published as open access, and its chosen license was CC-BY, then that gives you permission to reuse the work (including the attached source-code) so long as you provide attribution.  If the article in question wasn't published as open access, then you'll have to contact the authors or locate another source for the code that has clear licensing terms.

Unless the source code comes with a licence that explicitly allows you what you want to do, you have to get the permission of the current copyright holders to be on the safe side. These may either be the authors of the article, the publisher or both – depending on what copyright transfer happened between the authors and the journal.
However, it is very likely that the authors are fine with you reusing their source code; this may be one of their intentions for publishing it. Authors that have a problem with this, usually do not publish their source code. As a reusing of the source code raises the chance of the paper being cited, the journal is likely to endorse what you want as well.
Thus it is unlikely that anybody sues you, but on the other hand, if you write a mail asking the authors and the journal for permission, you are likely to get a positive answer (and they may consider to equip their code with a permissive licence next time).


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Co-author does not want biography+photo in paper submission
Some journals such as the IEEE Transactions on Aerospace and Electronic Systems (randomly picked) require a biography and sometimes also a photo of the paper authors.
Currently I have the case that a co-author working in the industry does not want this. He says (and I can totally understand this) that he does not want that possible future companies will find a photo of him when using a search engine. He also does not like the biography part but would accept this, if there is no other solution.
Question: Is it uncommon to ask the Editor-in-chief whether the biography and/or photos may be omitted? The journal would be a perfect match so that I do not want to pick another one just because of this.

Rather than trying to determine whether it is common or not to get the EiC involved in this matter, I would like to suggest that you ask a more "productive" question: are there established ways of handling the case when a co-author does not want to include a bio and a photo? The answer to this question, as far as the IEEE is concerned, is "yes."
Next to the author's name, simply state:

Randy D. Fuddles, photograph and biography not available at the time of publication.

Actually, you can find this in IEEE Editorial Style Manual: James A. Author (S’xx—M’xx), photograph and biography not available
at time of publication.

actually I've seen this in paper I was reading few days ago

updated link for the IEEE Editorial Style Manual

I can't really say that I "get" the concern of the co-author here, but I am aware that different people have dramatically different views on privacy than I do.
In general, this is definitely a question that you can ask the Editor-in-Chief without concern. However, depending on how many submissions the journal in question gets, it is possible that the EiC may be rather uncompromising upfront. For some top-level journals, submissions are a dime a dozen, and I have seen editors that see little need to engage in potentially time-consuming discussions with authors prior to even seeing an acceptable manuscript. Hence they may just point to an existing policy if there is one, without much further thought.
Hence, another possibility would be to just submit the paper regularly, and delay the problem until the paper proofing phase. If your paper is deep enough into the process that the question actually becomes urgent, it seems exceedingly likely that the editor and/or responsible persons from the publisher's side will be willing to compromise over such a triviality rather than reject the paper. For instance, they could allow your co-author to have a placeholder rather than his photo, and/or have a very short bio text along the lines of "Dr XY is currently a research engineer at GoodStuff Inc. For privacy reasons, no other information is given."

It should be noted that there are tons of IEEE papers where author picture and biography are missing because the author didn't provide them on time for publication. It is probably a requirement not strictly enforced.

My vague recollection from the last time I published in an IEEE journal is the bio stuff only comes in at final submission.

Would anyone know how this can be handled in Elsevier journals? I have a similar case with a computer science paper and Future Generation Computer Systems (the Elsevier journal)


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What background is necessary to do research in computational linguistics?
I'm getting ready to enter graduate school, and I would like to do PhD-level research in computational linguistics and natural language processing. I know that these two fields are very interdisciplinary and draw on various subfields of linguistics, computer science, math, and statistics. I also know that research in comp ling and NLP is done in different departments at different schools, with some schools having it in the CS department, and some in the linguistics department.
Ideally, what background knowledge should someone have in order to do research in computational linguistics or natural language processing? Which areas of linguistics, computer science, math, and statistics are necessary or helpful in studying comp ling and NLP, and is there one field among those four which is overall more necessary than the others?
(Note: per this question from Linguistics.SE, the distinction between comp ling and NLP is pretty blurry, which is why I mention both in my question.)

This question is an overhaul of my original, closed question. I put the current version on meta for feedback on whether it was on-topic before posting.

Conceptually speaking, I have a minimal amount of background with Comp Ling. That being said, I would feel that computer science is pretty high on the list of importance. The translation of languages to other languages is a major part of computer science itself, for example Java to Bytecode to Machine Code.

Multidisciplinary areas benefit from people with very different backgrounds providing their own point of view. Take it from a theoretical physicist undergrad doing a PhD in Bioinformatics.

@Compass My undergrad is in CS and I made sure to take compilers, programming languages, and whatever else would involve translation, and AFAIK you are absolutely right. I actually was curious how important linguistics and math were, but I phrased the question generally to get it reopened.

@tsleyson Every subject is arguably as important as you want it to be. I graduated with a BS in Bioinformatics, tried to get into medical school, and failed repeatedly. I eventually received an MS in CS, but I used my medical knowledge while doing software development at a research firm. That being said, you probably won't need more than basic statistics or math. Linguistics, I would think is more valuable due to how it covers the 'grammar' that holds things together, whether they be speech patterns or types of loops.

Linguistics Ph.D. admissions is unusual in that no particular background is necessarily required.  The reason is that many institutions do not offer a linguistics major, so the pool of linguistics majors is small.  In addition, linguistics is highly interdisciplinary.
To answer your question more specifically, if you want to enter computational linguistics, some programming ability is essential.  A bachelor's degree in any of the disciplines you mention may be sufficient.  I would also add psychology, anthropology, and foreign language backgrounds as potential entry points for a linguistics Ph.D.  You must also be prepared to learn statistics.

Based on your closed question, you already have an appropriate background for a Ph.D. program in linguistics, you just lack the appropriate grades.  So you should pick a master's program based on your interests and the program's placement history.

Thanks for your answer. So I should decide whether I prefer CS, stats, or linguistics, then pick a master's program and work hard to get the right grades, experiences, and recommendations for admission to a Ph.D. program. (I was already turned down by one Ph.D. program, but from what you say that was over my grades.)