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Referencing specific files in source code in a dissertation
I am making a statement in my dissertation based on a comment written in the Linux kernel source code. I would like to be able to reference this comment. At least I would like to be able to name the file to which I'm referring.
Is this (citing files in large pieces of source code) recommended?
What is the best way to go about doing this?

According to the MIT handbook in relation to writing code you should use the following when citing code.

Generally, the URL and the date of retrieval are sufficient. Add more details if it will help the reader get a clearer understanding of the source.
If you adapted the code, you should indicate “Adapted from:” or “Based on” so it is understood that you modified the code.

The page link above also includes the following in relation to open-source material

When you use code from an open source project, you need both to attribute the source and follow the terms of any open source license that applies to the code you are using.

Finally, as always with citing, you should check with your Department to see if they have guidance or a citation style-sheet.

It's not uncommon in certain areas of CS to cite specific files. In your specific case, I would suggest that you include the git commit hash of the kernel.org sources in the citation, so that people can find the precise version your referring to.


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Advisor offers phd early during master's thesis
I'm currently two months into writing my master's thesis, which is scheduled to take 12 months. During a conversation with my advisor he offered me a PhD position after I finish my thesis. He mentioned the possibility before already, but this time the offer was very concrete.
I already worked for my current supervisor in the past and did my bachelor's thesis with him and did most of his lectures. I always received good feedback. Since he was a new professor at my university at the time he told me that he wanted to find students to eventually to a phd under his supervision, so the offer didn't completely come out of the blue.
While I'm flattered by this offer it took my by surprise. I like the area of research but I'm still not totally set whether or not I want to pursue a phd (I'm leaning towards yes).
I also didn't look into different universities in my field of study regarding doing a phd yet. I feel a bit rushed by this question as the end of my degree will take at least another 10 months.
So I wanted to ask if my supervisor is early in asking me about a phd or if I am late in thinking about my (academic or not) future? I also wanted to ask for advice how to handle this sort of situation.
It's not like I wouldn't want to say yes, I'm currently at a good university in my field and my supervisor seems to have a good amount of funding. However I want to make an informed decision and somehow "test the market" and see if other supervisors would be interested in me as I did the majority of my "academic" work with my current supervisor.
I already talked to him about the offer and talked about some of my concerns and some details and he seemed to be understanding.

I've voted to close as it is an entirely personal situation. Examine your priorities along with the advice you get. It is up to you to pick a career and the path to get there.

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Math symbols at line begin
This question is a duplicate of this one I asked on graphicdesign.stackexchange.com, where commenters suggested to ask it here instead.
I am facing the following typography/formatting/spelling/punctuation problem:
In a scientific article I am writing, there naturally occur instances, where there are math symbols and their meaning scattered in prose text, e.g. "The input voltage u is given, as well as the inductivity L and the moment of inertia M, where [\n] i refers to the current through the motor." ("[\n]" symbolizes a potential newline character inserted by my teypesetting system.)
On some ocassions, my typesetting system sometimes inserts a line break before  the math symbol, putting the symbol at the start of a new line.
Note, that I am not talking about the start of a sentence, but just the start of a line.
My supervisor tells me, this is bad practice, and that lines must not start with a mathematical symbol (1).
I know how to avoid this in my typesetting system (LaTeX), but I have never heard that rule before, so I am curious about learning more  about it.
Questions

Can you guide me to a reference work to confirm or abnegate (1)?
If not a reference work, can you give an article where this is being written about?

If this is language-dependent: I'd like to know in particular about German, British English and American English.
Research
I am not well-versed in typography literature, and my online search has not brought any meaningful insights for me.
In an answer attempt at graphicsdesign.stackexchange.com, the AMSMath reference guide Part 1, Chapter 1, 12.5 Wording (page 81) has been quoted:

Try to avoid reference numbers, variables, equation numbers, and mathematical expressions as the first word in a sentence.

While this is just a suggestion, it is not strictly an answer to my question about symbols after line breaks, but might hint at the nonexistence of the rule in question.

This is just anecdotical evidence, so a comment rather than an answer: I've never heard anybody claim before that there shouldn't be a math symbol at the beginning of a line. Most math papers certainly contain many lines that start with mathematical symbols.

From my limited experience, I have also not observed this. Probably it would be best to confront my supervisor about his unjustified statement, if no further evidence for or against his statement is being presented.

From the academic point of view -  write the paper, submit it, and unless you find otherwise in instructions provided to authors,  let the editorial staff worry about typesetting to the journal's style sheet.

@ScottSeidman Your opinion generally seems like good advice; However, in this current scenario, I am the "editorial staff" who has been tasked to format others' texts into printed material.

Aside: Set your math symbols in italic. "The input voltage u is given..."

Hmmmm... the very first paper of mine I picked at random has symbols at the start of lines...

@GEdgar Thank you for the notice. Of course, in LaTeX I do so, but since this was not the focus of the question, I chose to omit it here. I'm updating the question, though.

If you are using LaTeX it will compute the line breaks itself.  To avoid that line break, use this: where~$i$ refers to.  If these are always single-letter symbols, that should cause little problem for LaTeX to compute a good way to do it.

@GEdgar Thank you for the heads up, but as is written in the question, I know how to achieve this technically. The question I posed was about the justification (not in a typographical sense).

@JochenGlueck I wonder if this is a misunderstanding/misinterpretation of a different, more widespread convention: that sentences should not start with a math symbol. I.e. "The input voltage, u, is given by..." rather than "u, the input voltage, is given by...".

Rules, such as they are, in typography exist only by convention and by the acceptance or rejection by someone (e.g., a journal editor) of work that does, or does not conform to the rule. The so-called Oxford comma, or serial comma provides a good example; some journals and publishers follow the Oxford comma rule (i.e., convention), others do not.
More useful, I think, is to ask why it is frequently recommended that one avoid having symbols at start of a sentence, or start of a line. If, instead of searching the web for the narrow topic of "symbols at the beginning or and of a line", you instead search for different approaches that have been taken to choosing the position for a line-break, you will find a considerable amount of thoughtful material.
I searched using Google, with the words:

typography choice of position for line breaks

This article from the World Wide Web Consortium not only provides useful advice, it also provides useful insights and a good point from which to explore the issue further. It does not directly address the question of symbols at the beginning or end of lines, but I think you will see that the question about symbol positioning fits within a much larger framework of thought about how to make text easy to read.

Thank you for your insight. I will have a thorough look on this article, but you also confirmed the conventional character of such rules.
In the meantime, I have had a talk with the mentioned supervisor, who backpedaled a bit and acknowledged your position as well. I probably am going to follow his conventions, now knowing that it is well within the rules of scientific writing do do otherwise, if I desire so.

+1 for the frame change - the point of typographical conventions is readability.

As you note, the AMS is entirely agnostic about lines starting with symbols, and gives little advice about linebreaking around symbols, in general (on page 103 of the AMS Style Guide, the editor is advised to "Avoid breaking math in text between fences,"—this is expanded upon on page 115; indeed, section 13.16, starting on page 114, gives a lot of advice on breaking equations).  That being said, the AMS Style Guide gives many, many examples of mathematics being broken across lines (both in inline and in displayed mathematics), hence it seems that the AMS has no problem with mathematics (and, therefore, symbols) starting a line.
The AMS Style Guide extensively cites Ellen Swanson's Mathematics into Type, which gives much the same advice.  The table on page 47 is, perhaps, particularly relevant.  Again, there are guidelines for breaking inline mathematical expressions and equations across lines, which necessitates starting some lines with symbols.
Generally speaking, the goal should be to avoid breaking lines in the middle of a "word" (which, as CrimsonDark notes, is a complicated issue.  If a symbol is the first character of a word, then a line might start with a symbol (e.g. it is better to break "the bag weighs 47 pounds" before, rather than after, "47", since "47 pounds" is, more or less, a single syntactic unit, i.e. a number with units).  On the other hand, a lot of people find single-letter variables at the start of a line to be "ugly" (I would include myself in that group—in many cases, these kinds of breaks also break up semantic units in an ugly way).  Thus, to a person who finds single-letter variables at the start of a line ugly, the text

The input voltage u is given, as well as the inductivity L and the moment of inertia M, where i refers to the current through the motor."

is preferable to

The input voltage u is given, as well as the inductivity  L and the moment of inertia M, where i refers to the current through the motor."

Note that, in either case, if you are using LaTeX, you can use ~ as a nonbreaking space, i.e. inertia~$M$, will prevent a linebreak between "inertial" and "M".  And, to be clear, this last bit is entirely a matter of taste and personal preference—I can find no style guide which seems to have much of an opinion, one way or the other.
All of the above having been said, this seems like something to not get overly precious about.  At the end of the day, most of these "rules" are just guidelines, which only really matter if an editor or supervisor is insisting on one version or another.  I see no problem with just using basic TeX / LaTeX, and letting the typesetting engine decide what to do.  If anyone complains, just say "Hey, if it's good enough for Knuth and Lamport, it's good enough for me." ;)

I largely agree but I don't think there is any problem at all with single letter variables at the beginning of a line per se. For example, "If such and such holds, then [line break] $X$ is a compact space" is perfectly fine. As you say, the problem is with instances like "the compact space [line break] $X$" where you break up a syntactic unit that belongs together.

@AdamPřenosil Indeed.  I tried to be careful to say that this is a matter of preference.  Personally, I really dislike starting a line with a single letter variable.  But this is completely a matter of taste.  And rules for keeping syntactic units together should definitely take priority over more arbitrary rules like "don't start a line with a single letter variable.

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Citation acknowledging contradiction
How do you acknowledge contradictory citations? Which (if any) of the following examples would be acceptable? (My field typically has citations at the end of the sentence, so I'm finding it even more difficult to achieve this.)
example 1, making a statement that is not entirely true:
"There has been relatively little research in diet overlap of extinct animals (but/although see Smith 2007)"
example 2, acknowledging that a study has inconsistent conclusions to other studies:
"Many studies showed coexisting animals had little diet overlap (e.g. Merry 2018, but see Jones 2002)"
example 3, studies are more or less equal in opposing results:
"Studies on modern animal diet overlap have inconsistent results (Jones 2002, Merry 2018, Smith 2007)"
I've found fairly clear guidelines on how to use "citation signals" in legal writing, but this is for my thesis.

If no one is strictly forcing you to only use citations at the end of sentences I wouldn't constrain yourself to that convention at the cost of clarity.

Following on from @BryanKrause, if they are forcing you to cite in such a restricted way, you could split the sentence into two, point and counterpoint: "Many studies showed coexisting animals had little diet overlap (e.g. Merry 2018). In specific circumstances [define] overlap was  shown (Jones 2002)"

I would recommend being clear and actually telling the reader what your citations say, not only that they exist. I always find it very unhelpful when a claim is made in the text and supported with three citations, but I have to look them up myself to see what they actually said. (Unless I want only assumptions about what they say.)
Example 1:

There has been relatively little research in diet overlap of extinct animals. One of the rare studies is Smith (2007), who found that Tyrannosaurus Rex and Homo neandertalensis had a large overlap in breakfast cereal consumption.

Example 2:

Many studies showed coexisting animals had little diet overlap (e.g. Merry 2018 comparing Pteranodon and Allosaurus). However, Jones (2002) found a large overlap in the consumption of humans between Tyrannosaurus Rex and Velociraptor mongoliensis.

Example 3:

Studies on modern animal diet overlap have inconsistent results: Jones (2002) found little overlap in frosted flakes consumption betweeen cats and cows, whereas Merry (2018) and Smith (2007) found large overlap in rice crispies consumption between cats and dogs, and between parakeets and humans, respectively.

Of course, this is heavily colored by the fields I am active in. If this kind of writing is uncommon in your field, this may be jarring to your advisor. I would suggest you keep this approach in mind when you read the next two or three papers and see whether this is sometimes used, or not at all.

I strongly agree. If this kind of writing is uncommon in your field, I recommend you do it anyway, as long as you have space, because it is helpful to the reader (even though these three examples would be better without the jokey aspects)

Example 2 could still work forcing the citation to the end if required.  It wouldn't be as nice, but could be done (e.g "However a large overlap was found...(Jones, 2002)")

@StephanKolassa
Thank you, this is very helpful! The examples were clear enough to push away my self-inflected confusion. I also appreciate your amusing examples!
For comparison, do you have an example of how/when (but see Jones 2002) would be used?

You could still use a "(but see Jones 2022)" if you just made a point, bolstered it with a citation, and wanted to call out that Jones (2022) differs... somehow. I would still say that it would be more useful to the reader to make explicit just how Jones (2022) differs from what you wrote before.


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I have the topic, I did my research, now what is the next step to write a literature review?
My Ph.D. supervisor assigned me a literature review paper to complete on a topic that I choose. I know very well the field and I did the necessary research, downloading every publication that I found on the topic. Nonetheless, I am feeling a bit lost since I don't know if there are guidelines for conducting a review paper.
Should I have a target journal for the submission before completing the review or should I choose one after the completion of the paper? I ask since maybe every journal may have different rules on review papers.
Are there rules that I can follow so I can fulfill the review's goals and not veer off into irrelevant details?
Thanks to everyone who may help me see light at the end of this tunnel.

This would be good questions to ask your adviser!

I don't know the status of the author, but in my opinion, review papers shouldn't be written by PhD students (or perhaps early career researchers).  In my field (machine learning) it requires considerable experience (not just knowledge or intelligence) to judge the value of competing approaches to some particular problem.  These review papers are commonly used by students and it is vital that the evaluation is very solid.  I think it is a job for experts (or better still, groups of experts) who have used all of the methods and made mistakes etc.

That is not to say students shouldn't be writing literature reviews - it is a good activity, it is just they probably shouldn't be submitted for publication in journals.  Coverage is also an issue that requires experience - I've seen some literature reviews on neural networks written by students and you would think from reading them that the field started less than a decade ago ;o)  Not the student's fault, there are advantages and disadvantages to both ends of the age scale!

@DikranMarsupial A researcher can be both an experienced clinician or supported by an experienced clinician and a junior researcher at the very first step of his/her career in research. Nonetheless, the topic chosen for my review was the result of other research that I am conducting by myself. My question, posted here, has the purpose to gain more information from senior researchers, if it is possible from different fields, about how it is appropriate to conduct a review, with a step-by-step approach.

@Heart That is why I wrote "I don't know the status of the author" the point I was making is that reviews shouldn't be written by people without experience.  Unfortunately it is very common these days for reviews to be written by students simply because they have to write a review anyway as part of their training so the supervisor is trying to get some added value from that effort.  Unfortunately it is not always added value for the audience.  I wrote it as a comment because it is a useful caveat but not an answer to the question.

If possible, try to check whether you local university library offers courses / classes for that. In addition, there are some good Youtube tutorials out there for beginners. Take hand written notes of every article you read, summarizing key points and publication details. This will help you to detect patterns (e.g. outcomes) that are worth reporting / considering. Good luck!

If you have a (potential) journal in mind. Read some of their review articles and try to abstract from that what works there. Perhaps do the same for a different journal in the field. Ask yourself why certain elements were included.
The details depend on the field, of course, but you probably want to cover major results, trends, typical methodology (and exceptions). The outlines of the various papers might be enough to get you started.

In my experience, is a good idea to know some examples from related reviews and articles publish in specific journals. Some journals have a guide to admitting proposals. Without knowing what is the specific topic that you are working is a little difficult to do precise guidance, nevertheless here you have an open-access article related to a methodology to make a literature review.


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If I get a HE fellowship do I still need a PGCert for academic practice or equivalent to become a lecturer?
I have a PhD and have been working as a researcher and associate lecturer in a UK University. I want to become a Lecturer. I have the credentials for a higher education (HE) Fellowship and some for a Senior Fellowship. If I manage to get it do I still need a PGCert (postgraduate certificate for teaching in Higher education)? How difficult is to get a HE Fellowship?

I would be helpful for an international audience to spell out some of your terms.

You should check the role descriptions for a lecturer in the particular university you're interested in, but I believe it's common that a Fellowship of the HEA (or whatever it's called now) is acceptable evidence of teaching qualification in most places.
I don't think either most of the PGCert classes or the HE fellowship application are that demanding. Applying directly to a HE fellowship requires a bit more documented evidence of previous teaching experience and a variety of bits of reflective text, but it's not too onerous, especially if you have someone who's done it before to provide you with some guidance. PGCerts are simpler if you don't have much previous experience.
Our university at least in principle supports either route, although I think the PGCert is heavily favoured, at least in more research-intensive areas where people are doing limited teaching.


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Does generating a DOI for my thesis using ResearchGate prevent me from publishing it afterwards in a journal?
I'm considering generating a DOI for my thesis, but I wondered if this would be a problem if I wanted to write a paper out of it.
Theoretically, the paper would not be exactly the same as my thesis, but it would be pretty similar.
I've found equivalent questions here, but none of the responses were actually conclusive.
Does it depend on the journal, or there is no problem whatsoever?

For clarification: Does getting a DOI imply that the document can be found and downloaded online? Or: Is your question specifically only about getting a DOI, or about publishing the thesis online with a DOI? To my understanding, you could get a DOI for a printed copy of your thesis in the university library.

Excellent question! I was concerned only about the DOI at first. I thought that the copyright problem would arise only if the document had a DOI.
However, based on what Serisano and Alazon said on their responses, having attributed a DOI to the thesis is a minor factor. What actually matters is if the document is available elsewhere.

You say "Theoretically, the paper would not be exactly the same as my thesis, but it would be pretty similar." Maybe this is dependent on the field and/or your institution, but a journal paper and a thesis are usually quite different. A thesis usually contains a lot of background and a wider scope, where a journal paper is focused on what the new contribution is.

You're totally right, NatualLogZ! My research field is inverse radiotherapy planning, and there's indeed a LOT of background content. I totally forgot to consider it.

This is journal/field dependent but in general getting a DOI for your thesis (or posting it on a preprint server or university repository) should not prevent future publication. Many journals, at least in my field, specifically state that theses are not considered prior publication i.e., you can submit articles derived from thesis work.
You should check whatever journals you want to submit to first though, just to be safe.

If you say that the journal publication would be somewhat different, then it does not seem to be a problem anyway. And in any event, the publication would get a different doi, since it would be a different object. The doi identifies the "object", not the content.
Otherwise, I agree with serlsano's answer: it depends on the policy of the individual journal whether they would tolerate it that the text is simultaneously available elsewhere. Assigning it a doi would somehow enhance the online presence of the manuscript, but that's a minor factor. So, yes, please check with the journal.

In principle, there should not be a problem. The DOI is a persistent identifier that will label your work as a thesis; ensure that your institution doesn't automatically assign dois to the thesis. Thirdly, I'd suggest that if you are only interested in the doi, consider for-profit vs. non-for-profit organizations e.g. Zenodo.

They are totally two different things unless you are going to submit the same thesis to the journal.


text:
Will a C+ on one major core class greatly affect CS masters admission?
I am interested in applying to some MS Computer Science programs in the US and my official GPA is 3.95. I went to a T20 private university in the US for undergrad, but in my freshman year I had a terrible professor for data structures + a heavy workload, and I was also generally just figuring out college at that time as an international student. The consequence was that I received a passing C+ on data structures. But from sophomore year to graduation, I have managed to get almost all A's on all my classes and maintained a good GPA in the end.
I am really scared that because I got a really terrible grade for one of the important CS fundamental classes, this will greatly impact my grad school applications. I understand that there is nothing I can do now except just try to strengthen other parts of my application. I did do a lot of internship and project work outside of school. Just hoping to get some insights from everyone here. Thank you!

I'd say you are a near lock to get into someplace, presuming you apply to a range of schools. But you have to apply to a range of schools, and enough of them. Just a numbers game at some level.

Yeah, C++ would be better...

@JonCuster I see. Thanks! Will definitely apply wide.

It seems unlikely that it would be a large factor, especially for a first-year course. But the competition can be tough in top rated schools.
In the US people tend to take a broad view of candidates and few things are disqualifying. In particular, letters of recommendation are very important.
It is what it is, however. But you seem to have recovered from the experience with a good GPA. Don't lose sleep over it.

Thank you so much for the great advice :)


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Am I eligible to do a PhD in the UK with 2.2 undergraduate degree and a 1st graduate degree?
I have completed my undergraduate degree in Computer Science with a grade of 2.2 (Lower second class) and a MSc in Robotics with a distinction (1st class). I have published a paper in an international journal during my bachelors. I am planning on pursuing a PhD in the UK. However most of the universities as for minimum 2.1 grade. Does my MSc score supersede my bachelor's grades? How can I get past the initial screening process where applications are weeded out if they don't meet the minimum eligibility criteria?
PS: I am an international student so funding is more competitive.

I was an EU student at the time, pre-Brexit so slightly different, but I got accepted into a PhD and shortlisted for a few other offers with a Master in AI with distinction and no paper at all. My undergrad was in CS but not relevant at all for academia, just goo to say I know how to code. I believe you have a good profile. But as semmyk-research said, depends on the school and university. I agree with contacting supervisor directly. If they are interested, they would probably use your grades just to check you are qualified

Bachelor 2nd class upper.
Masters 1st class
x1 journal publication (rating unknown)
Field: computer science

In the ordinary sense, your profile should be 'good to go' in getting interest from potential PhD supervisors in the UK. However, each department or school or university have their own dynamics and level of competitiveness.
If you're going for PhD within the Centers for Doctoral Training (CDT/DTPs), you'll be competing in a pool.
If you're interested in funded PhD projects, you'll still be competing but your research interest, your background, your personality and profile will become attractive attributes to potential supervisors as you'll need to reach out to them beforehand.
For self-funded PhD, your research interests and capabilities (#profile) might interest potential supervisors.
Take time to read more on CDT/DTP and its funding model.
PS: I graduated with a 2nd class lower (Engr'g) and an MSc (CS) equivalent to 2nd class upper and do not have issue attracting interest in PhD (CS, IS, Eng). Although I have publications and research projects under my belt alongside industry experience.
Even at that, I recalled that I had three PhD potential supervisors from the UK before getting my MSc result. I must admit, I had initiated and met with them while I was on a tour in the UK post one of my conferences. However, this was about two decades ago.

Thank you for your answer. I actually have a 2nd class lower and I'm an international student.

Your correction is noted. #curious ... is your MSc in the UK or your home country?

Yes, it is a UK MSc.

Technically your first class MSc will overwrite your BSc; formal requirements are normally good enough results in MSc or BSc, but not both (some may look at the later one of these so with a good BSc and bad MSc you'd be in a worse situation). Whether you win a place against competition is of course another matter.


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Receiving a Review Request from IEEE Transactions as a Ph.D. Student
I'm a Ph.D. student and trying my best to publish papers in IEEE Transactions.
I don't have any published work in the journal, except the one published in a journal in mdpi, and the one that has got a revision request from one of IEEE Transactions journals and been submitted again.
Recently, I got a Review Request from the other IEEE Transactions journal. As I looked at the paper, I felt confident in reviewing the paper and accepted the request. I think I did a good job in review.
However, I still don't understand the reason they sent me a review request, since the only publication I have is one in a moderate journal. The one is not even close to the topic of the reviewed paper.
Do they just randomly send the review request? Or, can a paper under review process make the authors eligible for reviewer?


text:
Choosing Recommendation Letter Writers: Relevance vs. Strength
I'm applying to graduate programs in mathematical finance, after finishing my undergrad degree in applied maths. I'm conflicted about who would be the best choice to write my recommendation letters: my finance professors or the professors from my machine learning and statistics classes.
The professors of machine learning and statistics are globally acclaimed with a 55-65 H-index, know me quite well, and are willing to write very strong letters. The finance professors, however, don't know me as well and are not as well-known.
Should I stick to relevance and choose the finance professors or would the weight of a recommendation from internationally known researchers hold more sway, even though their fields don't align perfectly with my study?

If you can submit more than one letter - do both.
However, if it isn't an option, I'd stick with the stronger letter (the profs from the machine learning). They know you better, they are more impactful in their field overall - and the field seems to me somewhat relevant. Imo, their letter would be more personable and hold more value, than the generic "I've seen this student on campus and he should be good" type of letter.
Alternatively, you could reach out to the students that have been accepted, and ask them how they got in.
Best of luck!


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Is it possible to work on your personal idea as PhD thesis?
I have come up by synthesis of 3 lines of research to a general idea whose questions and concerns and most importantly conceptual foundations can be addressed mathematically in a rigorous way.
Although I have not come up yet with any result but I can give N reasons why this framework that is only marginally, implicitly and partially alluded by 3 papers though never integrated and concretely formulated even as precise questions, is potentially a serious line of research.
I am a master's student of theoretical physics. Do you think it's anyhow possible to present a novel idea as your own PhD thesis subject matter?

Since you're in a master's program, I believe the typical course of action would be to try to work on your idea, or on part of your idea, as a master's thesis. If you accomplish something novel, then this would help you get into a strong PhD program, where you could continue working along similar lines.

@academic Not all Master's Degree programs include a master's thesis.

It's possible, but it depends on whether your supervisor estimates the idea is going to pan out enough to be worth being granted a PhD in the end. No supervisor particularly wants to have a student who just fizzles, and then they need to do extra work and time to get them over the line somehow, or perhaps have a bad administrative mark added to their record (not sure if this happens everywhere, but it does where I am). I personally figured out my own thesis project ('twas in pure maths) after the initial ideas suggested by my two advisor separately didn't seem to be going anywhere. YMMV.

What do you want to hear? Whether you can join a PhD program, have no supervisor, and just be left alone for 4 years to get on with it? Not really. Whether, once your supervisor hears your N reasons and agrees with you they justify working on that line, it's legitimate for the result of that work to be your thesis? Of course yes. Whether your supervisor actually will agree with you - some website can't tell you :-) Whether your supervisor will at least listen and assess? Depends a bit on the supervisor, but you're not there as a servant just to research what you're told to.

Basically I'm a bit worried by the "independent-researcher" tag on the question. If you mean, "can I get a PhD without joining a PhD program, just by doing really good work", then I think the answer is theoretically yes, it could happen, but practically no it won't. Nuts and bolts: your relationship with the university that agrees to assess your PhD makes you not fully "independent". Ask people at your current university, "here's my idea, how do I go about finding a PhD program where I can work on this?"

Also worth noting that many people do work on other projects while doing their PhD work also.

But it sounds like normalising systematic slavery! Doesn't it? @JoshuaZ

@BastamTajik Uh, no? You volunteer to do it, and you can quit at anytime.

And how much can you do creative work apart from Publish or Perish? Quit and ruin your résumé for the next application. For creative work one either is born to go to MIT, or must compete to hell so that the beauty and practice of science fades into oblivion or you find the right connections to Cambridge or Oxford to be heard only once, and even later there's no easy chance for grants and research. @JoshuaZ

@BastamTajik You can of course still do creative other work. I published a paper separate from any of my thesis work when doing my PhD for example. You are correct that if you quit a PhD program, you aren't going to have good luck getting in others. That hardly makes anything "slavery." As for your last sentence, I'm not even sure what your point about Cambridge and Oxford is or what it has to do with anything under discussion.

Oxford, Cambridge, ETH or Ivy League etc are where research is determined and the rest of universities must follow the lines of research determined by these elite research groups. Of course it's not always the case but mostly true. All the other research groups and camps with opposite or independent ideas become marginal or rendered obsolete unless they have enough local support. The algorithm is quite that of marketing and business. Of course you can publish your own ideas, but it might be recognised if at all, after your death! @JoshuaZ

So the only way out is to act like Trojan horse, penetrating and mastering one of the dominant research groups to be recognised first and only then try to establish independence! Which is pretty much huge waste of energy and time and mental health@JoshuaZ

@BastamTajik I cannot directly speak about theoretical physics, but I can definitely tell you that in closely related fields, including relevant areas of pure math, your idea of the elite schools somehow dictating things is just not accurate.

It's not dictation, it's rather publish or perish. It's marketing. There's no force, but you gotta get yourself convinced. Work for someone else or get others work for you. @JoshuaZ

Let alone the plethora of red herring, fake, repetitive, plagiarism etc articles dominating the main stream research in the name of collaborative work. What happens to the neuro-divergent mathematician who cannot get herself convinced with a work whose first principles do not convince her? Are we going to prescribe ritalin instead of supporting her to write formal work in criticism of the main stream which God knows how helpful her work is even to the criticized field itself. I can give several serious instances of such cases.

Pay attention that the researcher cannot know the quality of a theory prior to getting involved in it, and when involved, one already has lost major chances of changing route doing the wrong PhD!

The short answer is - yes.
A slightly longer answer is that from my narrow perspective, it is often useful to keep an open mind about what you’ll be working on in your PhD journey. Even if you believe your idea is novel, there’s a chance it’s either already known, incorrect as currently phrased, or simply unimportant. This is a statistical observation, not a statement about you or your idea (I don’t know either!). Most ideas turn out like this, and it’s important to recognize this.

Another possibility is that the problem cannot be solved (given what is known currently).

+1 the idea needs to be important to someone else as well...

@Stian It may not be important now, but may be found to be important later. Just make sure it is supported by your supervisor.

@CaptainEmacs ... in which case at least your supervisor needs to find it interesting/important. All I was saying is that it doesn't matter how good an idea you think it is, if you are unable to convince someone else it will probably remain unexplored.

Actually that's the problem. In the theoretical physics community, every field of research is predetermined. Even if I deliver any first results, then there's no guarantee that it can be taken seriously. I can give several examples where critical papers were ignored even up to 30 years and rediscovered by others. So I just want to know how realistic is to put forward a well-defined problem as subject thesis.  Is it waste of time to try to convince people to give it a chance? given that the medium of theoretical physics nowadays is quite utilitarian, which means publish or perish!

It’s not a waste of time, but the steps one needs to take from “I think I have a good idea!” to published thesis are many and risky at times.

@BastamTajik It really depends. There are some researchers that are quite open, you just have to search for them. More likely, you'll find them in Europe, especially continental Europe. Go to conferences, too, this is a good way to find people with shared interests.

@Stian Yes, you have to convince your supervisor. If not anything else, just to make sure your idea is not "crackpottish" and you remain grounded.

put forward a well-defined problem as subject thesis I would be surprised if a physics department considered simply formulating a problem to be Ph.D.-worthy research. You need to solve, or partially solve, the problem as well.

@BastamTajik I don't know enough of your field to judge really, but I'd warn that statements like "my supervisor is a dumb but publishes successfully!" "no one listens to me" "the entire field is corrupt" - or, more generically, a feeling that you are superior and everyone else in the field just doesn't get it... these are highly suggestive of crank-like thinking. It is highly unlikely that thinking this way will get you success in the field. At some point you need to be able to work with others and see how your work is inter-related in order for others to appreciate your contributions.

@BastamTajik Even if you talk about quantum gravity? Especially a talk-is-cheap subfield like quantum gravity, if all you do is “talk about” it. People have been talking about quantum gravity for about a century.

@BastamTajik As long as your modus operandi is to be rude and insult people, I suspect that you will have difficulty having your work accepted either by a Ph.D. advisor or by the physics or mathematics communities. Best wishes in your research.

@BastamTajik If your problem is of mathematical nature, indeed, go to math. It may be a problem, indeed, that much of quantum gravity work is essentially mathematics motivated by physics and/or with the hope of physics relevance, which may turn out not to be relevant in the end. That does not make it worthless. Maybe its importance is overhyped, but, again, that's not a reason not to work on it. The tendencies to push out other directions has been increasingly criticised from inside the community, but it is not a problem just of this field, but of well-funded fields in general.

@BastamTajik My opinion, however, is that, if you do not like what others do, make your proposal, find a niche where this proposal can survive, and go for it. If your strategy is to launch attacks on existing directions (whether justified or not), all you'll get is attention, and not of the good kind. Identify what you think is important, and identify what you need to get a supervisor to your side. If you need to switch fields for that, that's perfectly fine, as long as you are aware of the different culture/language.

Honestly, seeing your rude responses makes me slightly regret answering your question altogether. Deriding internet strangers who are trying to help you is not a good sign for future research relationships. Also if this is your actual name, posting these kinds of comments would be a red flag for advisors. I wouldn’t take you on if I saw these.

You will need to enroll as a Ph.D. student, get a Ph.D. advisor, and agree with your advisor on the outlines of your Ph.D. research.  Using research you have previously done may (or--more likely--may not) be possible.  Only your university can make the determination.

You need an advisor and then you can work on any topic for your PhD whatsoever if you can convince your advisor that this is a good idea.

I believe it is more typical that you find PhD advisor and project and only then enroll formally. Which makes it much easier in this case - you are skipping enrollment process until you know you will be able to work on that idea (or get told the idea is well-known already or won't work for X, Y or Z etc)

@quarague - although available funding may very well limit what you can work on. If  the grant money is for work on X, well, you either work on X or not get paid.

PhD student here. I have presented my personal idea to a potential supervisor and she liked the idea, so I enrolled as a student with that topic. I'm self-funded with a job in the industry. I have no working contract with the university and I'm not associated with any university project. Which means I don't need to respect any deadlines regarding projects, and I don't need to do anything for my professor regarding teaching or publishing.
So yes, it's totally possible.

Is this in the US? I would like to know more about how something like this works

This is Germany. My approach is unusual even here, so I'm the only one studying like this I know. The other PhD students are employed at the university and associated with a project. Feel free to ask me anything about this.

I am also very interested in this. How many hours per week do you work for your job and how many on your PhD studies? And how much do you pay your supervisor per month?

I'm also interested in this and I have lots of questions. Were you a student when you enrolled for the project? How did you get in touch with the supervisor? Is that the same university where you studied?

Hello Jannis, I work part-time in my job Mo-Thu, 32h, so I have 16h at the weekend for my dissertation. I don't pay my supervisor anything. I'm officially recognized as their PhD student and I heard they get some compensation from the university for supervising PhD students.
Hello Christian, I had the same professor as supervisor for my master thesis, so she already knew me. I was not enrolled for two years when I presented the project to her. So yes, same university as where I studied.

It depends
Having your own ideas is a feature of being a researcher, so this is in general terms a positive for your application.  A good candidate has ideas, and some sense of what a research project is - formulating a research question, working out what needs to be done to test it, devising a project to fit within the available time/budget/resources.
Of course many applicants don't have a lot of awareness about many of these things (eg whether your idea is good, potential methods, or how much time/budget will be required), and that's fine, you'll learn about that during a PhD.
So getting here at this stage is all positive.
However, it depends on sources of support - both funding and a suitable adviser.  Some of those may allow you full freedom (eg a personal scholarship) but others may want you to work on something else (eg an adviser with a funded project that needs somebody to work on it).
Hence you may end up compromising based on opportunities available to you.  Having your own ideas is often a positive sign in terms of an application for such a position, but being dogmatic about your ideas (even if they turn out to be of limited interest to others) may not be.  It is up to you whether to stick with your idea (but have no adviser or funding, potentially a dead end) or take a position that is interesting but not quite what you first thought of.


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How to publicize my rewrite of another group's software, should I try to get citations for it, and how would I attribute original authors
Four years ago, another group published a paper describing a new method for estimating an important parameter in my field. The method is theoretically elegant, has good accuracy in their benchmarks, and can be applied in cases where every other method I know of gives unreliable estimates.
The authors provided a GitHub repo with the code they used to realize this method. Unfortunately, the code in the repo is very poor. Several scripts do not complete successfully without fixing several lines of code; a key step in the pipeline is left as an exercise for the reader (notably, the paper stated that code for this step would be in the repo); as written, the whole pipeline requires the user to manually run many different scripts in succession; and the code is very inefficient, with e.g. computationally intensive calculations done to define objects that never get used. (The first author was a master's student, which might explain some of this.)
According to the citations of the parent paper, it seems that this method has only ever been used by the same group that wrote it, likely because of the limitations above. The issues page on the GitHub repo demonstrates that a few other people tried to run the code before hitting multiple serious errors and apparently giving up. After a lot of effort and fixes, I was able to run the code, and confirmed that it gives good results in cases where every other method fails. I also decided to reimplement the method almost from scratch as an evening project across a couple of weeks. I would like to believe my rewrite is an improvement: among other things, the runtime is much quicker (e.g. one particular step now takes 10 minutes rather than 40 hours), it takes a greater variety of file formats as input, and the whole process can be run in a single command. I have tested it on multiple machines and Linux distros and confirm that it does actually run out-of-the-box on all of them.
I think it would be good for my field to be able to discover this implementation of a useful method which nobody else has been able to use to date, and to be honest it would also be nice if I could somehow get recognized for this work. I really do think that it would satisfy a significant unmet need.
My idea right now is to put the method up on... JOSS? Zenodo? A preprint server? so it gets a citable DOI. (The venue to publicize this on is another question - I think it would be difficult and unnecessary to somehow turn this rewrite into a more traditional research paper.)  But I'm not sure how I would attribute the original authors. I could reach out and offer to make them co-authors on whatever citable DOI I create. I could leave instructions on the GitHub repo to cite both the rewrite's DOI and the original paper when using it - although in practice I think many people would not bother citing both. Or am I wrong for expecting citations for this kind of work? After all, I did not add any functionality, I just made an implementation that is more flexible and much easier to run at all. Should I just make the repo public, tweet about it, add the repo as a line in my CV, and be done with it? I did not get to my current position via a traditional academic route, so I am not as familiar with the norms around publishing and so on.


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Ethical Dilemma: Can I Publish as a Single Author?
A couple of years ago, a colleague and I collaborated on a research report where we each collected a different set of data for our report. At the time, I conducted a set of interviews with one group of participants (school teachers) and my colleague conducted interviews with a completely different set (college profs). We each analyzed our data independently and wrote our own part of the discussion section pertaining to the data set we collected. The result was a research report that we presented at a conference and which we never published in a journal.
My question is: would it be ethical to write a new paper based on the data I collected and excluding my colleague's sdata? Of course, I would have to modify the whole paper starting with the research questions to the literature review and other parts of the paper as well. In other words, I would write a 100% original paper using data collected for a different study. What is your take on this? I appreciate the responses!

Choosing the research question after the data is collected is another kind of misconduct. Avoid that.

@DanielHatton, no, I'm not. Don't mischaracterize how grounded theory works. It doesn't use the data that "sparks" the question to also settle it.

Presumably you designed the experiment together. That makes it a joint work. The best way forward is to find a way to work with your co-author on the paper.
In an extreme case, but ethical, you could write the paper yourself, list both of you as authors, and just get the other person to approve of it. More work for you, of course, but it avoids all the pitfalls.
But, perhaps in seeing a draft, they will decide to contribute more.
If you are willing to state a research question that depends only on your own ideas, re-define the methodology, and then re-gather data to test it is another way forward, that might only require acknowledgement of the other person's early contribution. But the existing data is tainted at this point.

See: https://en.wikipedia.org/wiki/Data_dredging

It might not be ethical. If you and your colleague discussed the questionnaire design and the methods you would use to analyze the data then even though you are using only your own data this new work is not yours alone.
If you are simply reusing your data to try to address a different question it is probably OK.
You should discuss how to go forward with your colleague. Perhaps just an appropriate acknowledgment in a discussion of the history of the previous project would do. Perhaps coauthorship is really called for.

Thank you so much for your answer. Such a good point about the importance of writing new a research question: that is exactly my intent as the single set of data I collected would answer a different kind of question than the two sets together. Regarding the instrument, we each developed a different instrument to target each group of participants, so I would say the labour on the original report was divided vertically in half between us.

See my comment on the question, please.

Sorry, but much of this is wrong. The second paragraph and the second sentence of the third.

See: https://academia.stackexchange.com/q/60393/75368


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Does interdisciplinary research usually require reading/reviewing more literature?
This may be quite a difficult question to answer in general, but I suspect that the answer is "yes" as less-well-defined discipline boundaries mean having to read more to cover all bases.
Can anyone with experience of both within- and across-discipline research weigh in on the matter?

I think the problem is not so much reading and assimilating the literature, but rather finding what is important and relevant across multiple different fields. It will be hard enough to keep up with what is happening in your own specialty; how much harder will it be to keep up in multiple fields! Solution: don't try to do everything yourself, but build a network of experts in other disciplines who you can collaborate with. And let everyone do their own reading (with frequent high-level exchanges).

@StephanKolassa How would a interdisciplinary graduate student build a network of researchers to write their dissertation and let everyone do their own reading? Doesn't seem realistic to me. My committee is absolutely interdisciplinary but they would kick me out if I asked them to do my readings.

@Shion: if your committee is interdisciplinary, you already have contacts, which is great! Go talk to your committee members' grad students! Of course, everyone should start looking for collaborators at his own hierarchy level. (And make sure all supervisors are fine with interdisciplinary research taking up capacity - maybe you can turn this situation into a grant proposal?)

Caveat: I am a current graduate student.
I have a very interdisciplinary committee. My home department is information science and my committee members are from electrical and computer engineering, communication and statistics.
My research stands at the intersection of social network analysis, privacy and surveillance studies and spatial statistics. I defended my dissertation proposal late last year and my literature review was ~50 pages with over 250 references drawn from 6 disparate areas.
Some of my other colleagues who work in Human-Computer Interaction (HCI) (itself a rather interdisciplinary field) have lit reviews around the 40 page mark.
I constantly feel that there is always more to read and really important classical literature on privacy (dating from the 1700s) that I should read but haven't read in depth.
Before, committing to a dissertation in this field, I used to work in theoretical statistics, specifically estimation theory. My readings were focused and significantly lesser in number than the juggernaut that my annotated bibliography has turned out to be.
Perhaps, more pertinent, TOREAD folder used to have 2-4 articles at any given time. Now, that is anything from 8-10 in addition to 1-2 books at any given time.
Therefore, in response to your specific question, Yes!, it feels like I have to read more now that I work in an interdisciplinary space to "cover" all the bases.

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


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Nature "Communications Arising" how recent must the original article be?
Nature's guidelines for authors say that

Critical comments on recent Nature papers may, after peer review, be published online as Brief Communications Arising

What actually counts as recent in this case? One year? Five years? It would be helpful to know before initiating the communications arising process which begins with direct correspondence to the author of the original paper, so carries consequences which may not be worthwhile if Nature consider the original paper too old to be of note.

This seems like a question for Nature, not for Academia S.E.

I'm interested in the answer. Did you ask Nature, @SideshowBob?

Yes, eventually. Without naming the paper I said it was 5 years old and they said that is recent enough to consider a BCA.

@SideshowBob Thanks for your contribution. Did you eventually submit the BCA?

Never did; I decided to incorporate the criticism into another paper (which hasn't seen the light of day yet)

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


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Should I switch majors? How will this look on grad school application?
At the school I study at there are several majors for life sciences. I am currently in a program called Life science - origin of diseases specialization. This program is very similar to the general life science program but has several more requirements for this degree. I still have a few more to finish but I realized that these courses are hard and a waste of my time. Most of these courses that I have to do are Organic chemistry 1 & 2, cell biology, etc. Which as most science students would know are difficult and time-consuming. After realizing that I don't plan on going to professional school (med, dentistry, and pharm) and just want to go straight to masters or a diploma, these courses mean nothing to me.
So my question is, it better to switch the general life science major that doesn't require these courses. Doing so would let me have more free time to find research and volunteer opportunities and hopefully keep my GPA up. Or would it be better to just stay in this program and finish it since I'm already halfway there (I am going on to my third year of studies)? But doing so would give me less free time and potentially deflate my GPA as these courses are known to crush your GPA. The two correlate a lot so I won't be missing any prerequisites for the degree when I do make the switch.
Thanks for taking your time to read this :)

Masters in what? Anything life sciences related probably wants to see organic chemistry at the least.

What do you want to do when you're done with school? Is the "general life science" degree going to qualify you for that?

@JonCuster unfortunately I do not know and am having difficulties finding out what I want to do. However, lots of the programs I have looked at don't require these courses and prefer experiences more.


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Grad School Failure and Drop out
During the end of my first year of grad school we have to take a comprehensive exam (I am majoring in Microbiology and Immunology) Due to personal problems I failed my exam, now I get to retake it but I am worried that I might not have enough time to prepare well for it, especially that it's an old school type of exam where they ask very detailed questions about anything related to microbiology and immunology not just the things related to my thesis.
So if I fail I get dropped out of the program.
Any advice what can I do next with my career can I still find a way to continue in Academia?

Have you reassessed your commitment to graduate school? For what reasons do you believe it's an appropriate path?

First, make sure that the personal problems are settled and, if not, seek professional help if needed.
Beyond that you have, I think, only two options. The first is to beg for an extension to allow time for preparation. An extension might be possible or not. It might be more possible if people can sympathize with your problems.
The other option is to drop everything else possible and prepare. And this is likely necessary even with an extension. Don't let the door close. It will be hard to reopen.
You are in a hard place. There are no guarantees that you will be successful, but "clearing the decks" and hard work will, at least, make success more likely. No magic bullet here.
But there is no information here that allows career advice beyond a failure. You will need to evaluate your situation at that point. But make sure that the personal problems don't continue to affect your prospects.
As to the exam itself, make sure you say sensible things, even when you don't have a precise answer. Try not to say nothing for any given question.

+1 but the two points are not mutually exclusive. You should have a laser focus on preparing even if you get an extension. At this point, you should focus on studying and (to the extent possible) not worry about what may or may not happen.

@cheersmate, yes, of course. Let me edit a bit.


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Is it helpful for graduate school admissions to publish in undergraduate research journals?
I’m a fourth year undergrad majoring in math at a university in the US. I’ve been working independently on an elementary graph theory problem for a while and I’ve found some nice results. It’s not revolutionary, but based on some research I don’t think anyone has looked at this problem before and it seems interesting. I intend to apply for PhD programs in Theoretical Computer Science. While I do have some research experience with a couple of professors (that should hopefully lead to decent recommendation letters) and a strong academic record in math and computer science, I don’t have any publications. Would I benefit from publishing my graph theory work in an undergraduate research journal, or do only regular journals count? I appreciate any comments, thank you!

"Would I benefit from publishing my graph theory work in an undergraduate research journal, or do only regular journals count?" Are you choosing between an UG journal and a regular journal?

Nope, while I feel my result is interesting, I don’t think it’s deep enough to get accepted to a regular journal.

As someone who has sat on multiple admissions committees at the PhD level, any sort of peer-reviewed publication is viewed highly positively in the decision-making process. That said, undergraduate-focused journals are viewed as having a lower barrier to entry relative to regular (non-UG focused) journals, which is a proxy for the strength of the findings presented in the publication. Depending on your timeline, you could try a regular journal first and if it gets rejected, then try a UG-focused one. If your timeline is tighter for the applications, I would go straight to the UG-focused one.

In the US, everything counts. So, yes, it would be a positive thing to do this and list it on your CV if accepted.
Graduate admissions (doctoral) is very broad based and takes in to account many things. What a committee is looking for is clear evidence of the high likelihood of success of admitted students. Doing undergraduate research is a definite plus and having a publication to show for it is even better.
Doctoral admissions can be very competitive and few undergraduates have very much if any research experience. Fewer can show a publication.
Also, get a letter of recommendation from whoever advises/guides you on the project. Letters are also very important.
As Azor Ahai suggests (I think), a regular journal would be better if you can get accepted. Talk to your advisor about tradeoffs here, including likely time to publication.


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Are any college stamps required on the letters of recommendation for masters abroad?
My head of the department is not providing me any department stamp on the letter of recommendation stating that the letter head is enough and with it stamps are not used. I have no idea if it's correct or not but I didn't want to take chances with my LOR.  Thus, my main doubt is regarding this. Do I require any stamp of the department on the letter of recommendation for masters, to verify it's authenticity?

"I have noticed several LORs and all have official stamps" How did you notice them?

I have never seen an LOR with any kind of "official stamp". Transcripts are sometimes documented more officially.

Please do not be worried. You professor is right. You do not need stamps or markers or a public notary's endorsement.
I am in academia in the US and if we felt the need to verify a recommendation letter, we would just (1) look up the writer and (2) contact the writer directly. Mostly, receiving a letter from an academic email address containing a pdf with an institutional letter head establishes prima facie credentials.
When I write invitation letters for conferences so that participants can get a visa for the US, I do exactly that: an email with institutional letterhead emailed as a pdf.

I very often write recommendations for European Universities, especially Germany and the Netherlands, and no, no kind of stamps are required, only proper letterhead and contact information.
Note that in most systems the student does not see the recommendation letter. The recommender usually sends the recommendation directly via email or by a electronic system to the receiving institution.
For verification of authenticity, there are other methods if required, such as directly contacting the letter writer, or requiring specific measures like using institutional emails (no free email accounts are accepted). This is why the student is not directly part of this process in most cases.

But what if students  have to upload the recommendation letters themselves while applying?


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Is my GPA good enough for the graduate mathematics schools in the US?
I am an undergraduate engineering student in Azerbaijan, and my major is process automation; however, I intend to change it and study mathematics in one of the grad schools in the US. I received only A's in mathematics classes, which are Calculus, Multivariable Calculus, Differential Equations, and Linear Algebra. Currently, I have been self-studying more advanced mathematics branches such as Real Analysis and Abstract Algebra, also have written a research paper on Differential Equations. Nevertheless, I have mediocre and low grades in the engineering classes such as "Electrical Materials and Devices", "Electrical Machines", "Process Control", etc. My current GPA is approximately 3.55, and I am planning to take GRE and GRE mathematics subject tests. Does my plan seem plausible? Am I eligible to study in PhD program for mathematics under such circumstances?

Your main problem is not GPA but lack of graded coursework in some standard upper division undergraduate classes. As it stands, you will not be competitive in the top 50 graduate programs in math in the US, unless you have done something spectacular in your differential equations paper.

Thanks for your answer. Is GRE math subject test effective considering the gap in my coursework? I will try to write a few more papers on Abstract Algebra though.

Could be but you would be competing with other international applicants who would have stellar GRE subject....

What do you mean "have written a research paper on Differential Equations"? Is this a research paper that got published in a peer-reviewed journal? Or?

Yes, do take the GRE mathematics subject test.  You will probably also need to show  English abilities, say TOEFL exam.

Yes, I have taken IELTS and got 8.0 out of 9.0 overall

The paper is published on the journal of an international conference.

You can be considered, but note that doctoral admissions in US is broad based with letters of recommendation especially important. You are also missing some essential advanced courses that US undergrads usually take: Abstract Algebra and Topology for example. There are other common ones like Finite Math and Symbolic Logic.
There are some places that will let you make this up. But...
See this answer to our canonical question: How does the admissions process work for Ph.D. programs in Country X?

A GPA of 3.0 and above is usually the gold standard, at least in my field (physics), so it sounds like you are on the safe site. You may also consult with tools such as this, which easily allows you to convert your non-US grades to a 4.0 system GPA.

3.0 seems more like the silver standard, actually.

Totally agree, I meant that at least you make the cut

Thanks, the tool is quite helpful


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Will clicking on Google document mistakenly from other students in a class that I did not enroll in can be considered as academic misconduct?
I'm a visiting student in a public university in Idiana.
Last Feburary, March and May, a student from another class shared with me a Google document multiple times:

a group work from a course which I did not enroll in
which gave me the permission to edit the document.

However, I did not change anything as any change will be recorded in the google drive document editing history.
I just clicked on the link for curiousity.

Will I be in trouble with the Dean of the student on academic misconduct?
What should I do in this case as the grade for that course has been posted and I did not see any communication from university official?

I think you're missing something because none of this post makes any sense.

What I'm missing?

Why you think opening a document is misconduct, why you expect a grade in a course you're not enrolled in, why you're expecting a university official to communicate with you, why it matters that you have "permission to edit" the document, why it would matter whether or not you changed anything in the document, etc.

Yeah I forgot as I checked this policy and I'm quite worry: A student must not steal, change, destroy, or impede another student’s work, nor should the student unjustly attempt, through a bribe, a promise of favors or threats, to affect any student’s grade or the evaluation of academic performance. Impeding another student’s work includes, but is not limited to, the theft, defacement, or mutilation of resources so as to deprive others of the information they contain.

Did you do any of the things in that policy? If so, which one?

I asked my friend about it and he told me that: accessing a Google document for a course in which you were not enrolled, without proper authorization, can be seen as interference with another student's work. Reviewing the document without permission may be considered interfering with the privacy and integrity of the group work. However, I'm not totally believe in him

Another student invited you to take a look at their work and you did. That's not remotely an interference.

Thanks. What should I do in this case? Should I let it go or should I tell to that student ?

Nothing, really

What people consider to be X or Y is something completely up to them. We here can only talk about the standard of the semi-mythical "reasonable" person.
Looking at a document cannot constitute academic misconduct unless the reading was used to copy content in one's own work. In general, students should be encouraged to share their work with outsiders and even solicit feed-back.
In general, if you post to this forum, it is helpful to include your country and to more clearly specify your question and your situation.

+1 for the last paragraph

I'm in agreement with Thomas Schwarz.
In addition, kindly bear in mind, from a (info/cyber) security viewpoint, (finding out) that one has Access doesn't equating using Access. This is so when engaging confidentiality leg of the CIA of security.
The applicable Policy will be a decider.


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Should I stay in my current PIs lab for grad school?
Should I stay in my current PIs lab?
I graduated from a Biology program with a 3.49. During that time I didn’t take many quantitative classes. I look calculus 1 and I’m currently competing a data science certificate. Afterwards I got a wet lab job. I do a bit of data analysis, and I have three non-first author papers and a poster but none related to bioinformatics. I was considering applying to Bioinformatics PhD programs next year, but was offered the chance to stay in my current PIs lab. Her background is imaging, and her lab is more nutrition/neurology focused but she did have two Computer Science PhD students in her lab as a co-mentor, and she is affiliated with the data science department. From what I heard they did struggle a bit because she doesn’t know how to code and wanted more data science from them which  wasn’t applicable to their degree.
She is considering a collaboration with another professor who is actually a bioinformatician and is using causal analysis to analyze behavioral sensor data. I would only join this project if I stayed as a PhD student. I do like the lab, but I’m just not a fan of the small midwestern city I live in. I would like to live somewhere better preferably on the east coast, but I’m a bit worried that I wouldn’t be able to get in anywhere else in a better city.
Basically I’m wondering: with the information I gave, what am I lacking to apply to grad school?

Yes not fully, I’m worried I might close this for my telling her I want to apply elsewhere. But that question can only be answered by a discussion with her. Mostly I’m wondering if I have enough experience to apply anywhere else?

I suggest that you think long term. The location of the lab is only a short-term consideration. After your degree completion you will be in a better situation to move. Do you want to work in this field to begin your career? Is your success likely in this lab?
On the other hand, if you are completely familiar with the work this lab does and what the people there can offer you, there is an advantage in expanding your horizon. I usually suggested my own students study elsewhere in grad school, just to get, potentially, a broader view and to expand their contacts. That, of course, is a longer term way of thinking.
But, think about your career and your future more than your current, perhaps boring, living conditions. Is this the best place for your career? Maybe it is, or not.
A discussion with the PI might be useful. And, if you can enhance her career with your skills, creating a better collaboration, it might also be to your benefit long term.

With three publications (non-first author) and a poster you're in the "good enough" category in my department. That is, your selection will depend on other things, that's neither disqualifying nor "so good we have to take them".
You will have to apply to grad school in any case (though if you've been offered a chance to stay, that means they plan to accept you), and I can see no reason why you shouldn't apply to others as well. I suggest looking to see if there are faculty at other institutions that are already doing what you want to do, rather than the possibility that your current advisor is thinking of working something out.
If they were so controlling as to make the offer contingent on you not applying elsewhere, I would see that as a reason to leave in itself.
And this will work very nicely in your application: "My undergraduate research was in XYZ and I believe that this kind of work is ripe for study with ABC technique. I would very be interested in working with Professor Blah  in applying ..." Or "My work was in XYZ and I realized that I needed experience in ABC to proceed. I would like to ...".
As far as location goes, I would not recommend staying in a location you don't like unless you get a specific benefit from doing so. The only advantage I hear in your situation would be working in the lab even more than most graduate students (which is already "all the time") to get out faster.


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Do we need to pay for author registration at a conference to present our paper at an non-archival workshop?
My paper recently got accepted in a non-archival workshop at a prominent computer science conference. Since it is non-archival, should I still pay author registration (which is between $500 to $1000) to do a virtual oral paper presentation that is less than 15 minutes? That seems like I am paying for the merit to present my work at the workshop instead of my work being worthy enough to be presented...

Related: Why do we pay to present at conferences? Whether it's worth paying that much, especially for virtual attendance, is a personal decision, of course.

There’s no way to answer this. It really depends on the conference.

You can register only for the workshop part of the conference and skip the main conference. This will cost considerably less.

Do you have the option of paying for the workshop only excluding the (rest of the) conference? For instance, I recently participated in one of ECIS' workshop without registering/participating in the whole ECIS conference because I won't have the time (and can't be on ground physically to engage my peers). Invariably, we all have different reasons.

Nobody can answer this question for you. It's like asking "Should I pay $1M for a Matisse?" The answer depends on two factors:

Do you have the money?
How much is having a Matisse worth to you?

The same applies to your question: Assuming you have the resources to pay in the first place, how much is presenting at this conference (and participating in it as well -- there are also talks to listen to) worth to you? We really cannot tell you, it's a question for you to figure out.


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Apply to top US chemistry phd program right after Bachelor’s degree without journal paper publication
I am a Taiwanese undergraduate student in chemistry studying in Taiwan (National Taiwan University). I want to apply chemistry PhD programs of top US universities (MIT, Stanford, UC Berkeley, etc) right after getting bachelor's degree. Although my target schools don't explicitly require journal paper publications, I am worried about my competitiveness compared to other applicants if I don't get one. So I wanna ask two questions as following supposing I get other factors done well (GPA 4.15 out of 4.3, TOEFL 105, and two years of research experience):

Do most successful applicants (like > 50%) have publications?
Are only papers in which I am the first author helpful?

Thank you for reading this somehow naive question. Thank you very much in advance!

In the US there is not an expectation to come into a graduate program with publications. In fact, it is fairly rare for an undergraduate to have a peer-reviewed publication under their belt (let alone a first author one). It would certainly make you more competitive, especially for top programs, but it isn't a requirement. It sounds like you already have a good application with plenty of research experience. That already puts you in a good spot - a publication is just the cherry on top at this point. As for being first author, that isn't necessary either. Having your name on any publication, regardless of position, is an accomplishment and will be helpful to your application.
Some unsolicited advice, don't get too caught up with name-brand schools - admissions are competitive and can be almost random (or at least they can feel that way). There may be a program out there that aligns with your goals but isn't at the very tip top of the rankings. Don't be afraid to search around to find a good fit. There are plenty of excellent universities to choose from.

No, without publications people can get admission
No, papers with co-author also can be helpful

Your answer #2 is a bit unclear. Do you mean "papers in which OP is not the first author is also helpful" ?


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Undergraduate with research partner issues/concerns
In the Fall I will be completing my last year of undergrad. Once I graduate I want to get my PhD, and so grad school applications are approaching.
I’ve been doing research with a professor at my university over the past year, and I’m continuing this research into the Fall. Generally speaking, it’s been going pretty well. I enjoy the research and it’s been productive. I’ve also been doing this research with another undergrad at my university.
I have a dilemma with him, though. Truthfully, over the past year, I have been much more serious about the research, have contributed all of the major insights, and written essentially all of both papers. Our research meetings (between me and him) essentially consist entirely of me explaining what I’ve been working on, and he does not really contribute to our conversations. He also sometimes says things which indicate to me he does not even truly understand the research problem. I’ve felt alone in this process much of the time.
I have put this past me, since I like him, and I know that what matters most is conducting meaningful research. However, a recent conversation with him and my advisor kind of sent me off the edge, and I am looking for advice about what to do moving forward. Specifically, he expressed that he wants to continue working with me on the research in the Fall (which I was not expecting), even though he will have a full-time job and many other responsibilities. I am not confident that he will be able to contribute to the research, given my experience over the past year when his responsibilities were much lower.
Further, my professor mentioned that working on research alone is better for grad school admissions. I am not from a top university and I know admissions are extremely competitive for my field. I now have this strong emotion, whether justified or not, that having my research partner’s name on our work…what feels like just my work...will damage my chances. This emotion only builds when I consider the research situation in the Fall, where I’ve cleared out much of my academic schedule for the research, and he has significantly more responsibilities to juggle. I don’t consider myself cutthroat, so I hate that I get angry when I think about the prospects of him being put above me in the admissions process because of this situation. The upside is that I’m pretty sure my professor knows I’m carrying the operation and hopefully this would come through in his recommendation.
My current plan is to talk with my research partner about these concerns tactfully (specifically the research in the Fall). However, I am nervous he will convince himself he will have the time and energy to contribute, for which I am not confident as mentioned. I also do not want to burn bridges, as it is not good professionally, I don’t want to create a division, and he is my friend. I feel stuck between a rock and a hard place. Does anyone have advice on this situation and maybe where my mindset is flawed?

Anything preventing you from talking to the professor about this? That would turn "pretty sure" to "absolutely sure" that he knows the situation.

This is something I've thought about. I guess I am nervous and as mentioned I don't want to cause a division. But those are not necessarily good enough reasons to avoid that solution.

I would consider having a chat with your professor about your concerns. Express your commitment to the research and get their take on how your research partnership might affect your grad school applications. They can offer insights into the admissions process and how much weight is placed on individual contributions. You could also discuss the possibility of working on separate research projects. Collaboration and teamwork are crucial, but don't forget to prioritize your own academic and career goals.
Having an open and honest conversation with your research partner is another approach. Share you concerns and express you expectations for the future. Communicate your perspective on the research and your plans for the upcoming Fall Semester. This could give them a chance to understand your viewpoint and possibly reevaluate their own commitments. Discuss and possibly establish what your expectations are for your research collaboration moving forward. Determine the level of involvement and contributions expected from each party. It's essential to have a mutual understanding of the responsibilities and time commitments required, especially considering your partner's full-time job and other obligations.

These situations can be frustrating. Group projects (research collaboration included) never really change. Sometimes people just don't put in the effort and still expect to benefit. So on one hand, it is not cutthroat to fight for proper acknowledgement of your work. On the other hand, it is very cutthroat (and arguably rather unethical) to push someone off of a project without giving them a chance to contribute properly. So, while your concern about this other students current contributions (or lack thereof) is reasonable, it's not necessarily fair to push them out because you think they will be busy during the coming semester and it is almost certainly unethical to push them out solely to benefit your application.
The correct way to resolve this would be to give this person a chance to remedy the situation i.e., begin to contribute to a more reasonable level. If they still do not put in work then, and only then, should you considering having them removed.
In your case, I think you should talk to your professor. Express your concerns and see what they think. You mention your "pretty sure" your professor knows what's going on. So just have a conversation.
On a side note - it sounds like you are leading this research project. This can be really hard and the path of least resistance for inexperienced researchers is often to do everything yourself. This can lead to a situation similar to the one you are in. You do all the work and your research-mates seemingly do nothing. At some point (usually once people are independent researchers) this isn't an excuse. But undergraduate students almost always need specific tasks and instructions. Maybe you don't, but the average student does. So perhaps a solution is to just give your classmate tasks. If there is something that needs doing, ask him to do it rather than just doing it yourself. If he doesn't do the work, then you can go ahead and escalate.

"give this person a chance to remedy the situation" equally important is to set expectations. Be clear that you expect a certain amount of output.

I think that your instincts are correct, in that the other student is unlikely to change their ways. It's a sweet deal for them: you do all the work, they take vacations, give excuses (however reasonable), make promises (however heartfelt), and at the end, they get publication credit. Now they are making more promises, but once you accept the deal, you can count on them dropping the ball again. And why wouldn't they?
Two ways to solve the issue:
(1) Express to your friend that you'd like to have a sole-author publication, and that they suggest a way to split the project so that you work on your stuff and they work on theirs. They won't get anything done, but at least you won't feel the resentment that's currently eating at you.
(2) Set clear expectations, in writing, with clear milestones, and deadlines. Lots of small deadlines. They might realize that the gig is up and give up on the paper and let you get the sole authorship you want. Or they will start missing deadlines and with every deadline, you bring again Option #1, splitting the paper.
Whatever you do, you need to get out of the corner where your partner's promises of work result in publication credit.


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How do I write the methods and results section of a programming-related paper?
I'm new to this. I've written research papers before, but never one about a computer-science topic. So, I was wondering how exactly I should approach the methods and results section, as it seems more natural to simply do it all in one section, explaining how I did what I did and what I found for each step of my research. I'd appreciate some advice!

Before you write papers, you should read them. What do other people do in their papers?

Define 'written research papers' before - the structure and language of a technical journal article bears little resemblance to any paper you wrote in, say, your undergraduate degree. It is just a different style of writing.

In my experience, how to organize the sections for a computer science paper depends a lot on the conference or journal that you're sending it to.
With "computer science native" organizations like IEEE and ACM, there is typically free choice allowed for section titles, and thus no need to use a "methods/results" format.  I'll thus often end up with section titles like "Architecture", "Analysis", and "Experimental Validation", organizing things however I think will be clearest for a reader. This is what I recommend doing whenever possible.
Unfortunately, many "non-native" journals, such as those with biology or chemistry roots, will force you to map your paper onto a Procrustean bed of "Methods/Results/Discussion" or even putting the Results first and the Methods last. This can be really problematic if you view an architecture or algorithm as a method, because then you'd be presenting experiments with the algorithm before you presented the algorithm!
In this case, it helps to realize that in computer science the development of a "method" like an architecture or algorithm is itself a result! I thus tend to deal with the "methods/results" format by using the same structure as I would in a computer science paper, but turning all the sections besides Introduction and Discussion be subsections of "Results". The "Methods" section is then reserved only for the not-very-interesting details somebody will only need to know if they are trying to reproduce identical experimental results.  For an example of doing this, see this recent paper of mine on a software tool for biology.

Some fields, specifically math and CS, aren't like others and so it is natural to structure research result papers differently.
But the methods section should say something about how your program/system architecture differs from the standard techniques applied to your problem. The results section should show how your results are an improvement (or not) over the standard. Even if you don't show an improvement, you can give an analysis of how the new technique fails and still contribute to the literature. Negative knowledge is still knowledge, though you haven't indicated that is the case here.
And note that even small improvements can be important if the means to that end are novel and can influence future research.
But, assuming you have advanced the art say both how and why in the results, and maybe the conclusions, section.

I strongly disagree with your second paragraph, because of the "results before methods" inversion that many journals require, as mentioned in my answer. If you read non-CS papers in these journals, you will find that their equivalent "architecture" materials are also in the results section!


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Germany WiMi/PhD Studentship Hiring Process
I've just recently applied for a WiMi/PhD student position in Germany and was interviewed for it. I had to present my proposal and there were many questions related to teaching. The panel was a 4-person panel with 2 individuals from my specialism and 2 individuals from HR (one for disability and another for diversity/inclusion). Is this typical? They said the results would take weeks. How much time do they usually need to decide?
Thanks in advance for your replies.

To add to the time they usually need to decide: As Sursula said, this is different for each institution / research group. If this is important to you, I would write a friendly e-mail asking when you can expect a decision. If you have a deadline to make a decision (e.g., because of other offers) - it is totally fine to tell them (very friendly) and that you would thus, appreciate a decision until XY.

If they already said that the results would take weeks, there are probably specific reasons for that. For example, some candidates have a much later interview appointment, or the meeting in which they decide on the candidate to hire can only take place then due to vacancy.

Sometimes things can go very quickly, if all interviews are over and there is a clearly preferred candidate. However, that candidate might still reject the offer, and then second- and third-rank candidates might be invited. From their perspective, the process might take several weeks.

When I asked why it would take weeks, they said there are many people involved in decision-making. And I've never had a 4-person panel for an initial interview before, so I kinda believe them. Maybe more people or teams are involved in Germany.

Concerning the interview panel, this is normal - as there are laws in place to preferably hire people with disabilities and/or from certain underrepresented groups if they possess equal suitability and qualification. As this "equal qualification" is often not easy to evaluate (and sometimes the "able bodied white man" gets hired even though other suitable (more diverse) candidates would have been equally qualified), disability and inclusion representatives are included in university hiring processes to assess the qualifications of all candidates and then advocate for the person with disabilities or from an underrepresented group.
Concerning the time: this is pretty much depending on individual facors and does not necessaryly take that long, or might take even longer.

Thank you. It's good to know these policies on disability are in place. They were very thorough and wanted to know what aids I needed if I were to work there.


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Honours project: should I propose something of my interest, or pick from what offered by supervisors?
I'm from Australia
I'm about to start my honours in Computer Science. I aim to do PhD afterwards. My uni does not currently work on the research topic that I'm specifically interested in. Fortunately it allow us to propose our own project ideas.
But past students pointed that supervisors can be very perfunctory if I do not work on their projects. They tend to think that you are fully responsible to what you propose and provide minimal help. This makes me concerned. I'm totally new to research, I don't yet know my idea is really doable. If I'm on my own I might screwed up.
Should I follow my interest, propose my own topic, and aim for PhD in other universities?
Or should I put my interest aside, stick with what's being offered in my uni, so that I can at least get high grades and secure a PhD spot in my current uni? (But will it still be possible to apply for PhD in my dream topic?)
BTW I found that topic seems to be popular in Melbourne: RMIT, Deakin and SIT all focus in this area. Is it a good idea to email these universities to express my interest and ask him for what topic I should do to gain PhD spot in their labs? (But I imagine they have their own students to care about and won't be interested in me.)
BWT I talked to an old professor who worked in the topic of my interest. He has good attitude and will to supervise me. But whatever I say he just nod and respond 'Good, go for it'. I don't know how helpful he will be....
There's also a younger supervisor who is known to be pushy and responsible. But only supervise his own projects.

Unfortunately, this question is too broad, because the answer would depend on too many things we don't know: your personality, the personality of the potential supervisors, the projects, the traditions at your uni, etc.

Choosing a topic is one of the hardest things in research. What will you do if the topic you've chosen turns out to be a dud?

You seem to have laid out the options well, only you can decide. But I will point out that at this stage "you don't know what you don't know", so getting firm guidance from an experienced supervisor may well be worth it. A good research experience will always trump a bad one, regardless of anything else.

In any academic course, the correct choice is "whatever the professor says is the correct choice."
Therefore, the answer to the question

should I propose something of my interest, or pick from what offered by supervisors?

is almost certainly "pick from what [is] offered by supervisors."


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PhD Supervisor Jekyll/Hyde
I have a Phd supervisor who yo-yos between being overly critical and mean and then thoughtful and kind. I find it very confusing, as it's so inconsistent. I would hope that I am a good judge of character, but I don't know if he has the best intentions for me. I don't know if I should ask him  to be a reference for post-doc positions. What are some ways that you have handled working with your superiors who behave in this way?

Can you give examples for both kinds of behaviour? Perception and evaluation of behaviour can be very subjective, so it's hard to get a clear picture of the situation from the current content of your question.

In academia many share a value system that implies that you should be nice and caring to other persons and particularly your PhD students  but hard and critical when it comes to their work, as this is the best to ensure high quality. From the outside it is not always obvious to see when is the time for what. It may well be that the supervisor's value system leads to the kind of behaviour described by you.

How often is this yo-yo? In the same meeting?

Perhaps he has mental issues. It isn't unknown in academia. Perhaps he is going through something personal that is affecting his general behavior.
You might talk to someone else on the faculty (or another student, perhaps) who can give you some advice. The head is probably aware of such things and you can seek advice there, though don't make it a complaint.
An untenured advisor might be frantic about their own tenure case and behave inconsistently. And, "critical" can be different from "mean". Personally critical is not acceptable, of course.

"Personally critical is not acceptable, of course." Depends on what they're criticising the person for. If it's something like unprofessional behaviour or appearance, then that might be acceptable.

@nick012000, I wouldn't call that "personal", though.