text:
Sending a full Transcript, or only a part?
I have a quick question. I have to send in official transcripts to some graduate schools. I am trying to apply for Mathematics. However, since i am also doing a B.A in Philosophy and Economics, the last semester has no mathematics classes as I have some classes I have to take. I have the option to not disclose that in my official transcript and "cut off" the future semester. Would that be seen as disingenuous? I don't want the admissions to think I am "avoiding" mathematics, there is sim ply no math courses my school offers that I would like to take and I need some courses for my other majors.

Send in the full transcript. Just because there's a semester of no math doesn't mean they'll look down on it.

I have just one advise: Be honest. Changing an official transcript to make you look better is not honest, and could get you into trouble.
Moreover, a semester without math does not necessarily look bad.

Perhaps the lack of more advanced courses in your undergraduate program could be a point of discussion in your letter or essay? I agree with Sean Roberson -- send the entire transcript. If you were judged alongside another applicant and you each have equivalent maths coursework, the advanced courses in Philosophy or Economics may make you more appealing/interesting.
Have you reached out to the administrators and/or faculty in some of the departments to which you are applying? You can ask them their opinion on this, and other things. You could remain anonymous, or not. There's not much to lose and potentially a lot to gain by asking them these questions. Good luck!


text:
How to convey your full length paper in conference through slides?
I am a PhD student works in computer algebra(Theoretical computer science). I have published one research paper recently, I am currently making slides for the paper. It is my first time and believe me I am struggling a lot. I have spent 4 days but till now not able to convey the idea that I want to deliver to the audience. I have given 30 mins for the presentation. My algorithm is based on 4-5 other algorithm with few lemma and some modification to previous algorithms. I am confused how to make slides such that I can convey my work efficiently.
Should I focus more on modified previous results or on new lemma. Should I first explain them notations and definition or directly go to the results.
Questiom : How to convey your full length paper in conference through slides?
Edit : Audience is Professor and Ph.D students of computer science and mathematics.

Think about how you would dance your content.

Important information is missing: Who is your audience? How much do they already know about your topic?

some of them may be first time listening about algebra

I can read mathematics, if motivated and given time with nobody talking to me. I can also recognize some common formulae, and understand small variations. Notation you have to introduce would do me no good at all. Ideas and intuition might motivate me to study your paper.

In a short face to face presentation, remember that insight is much more important and valuable than detail. People aren't going to remember the detail, and can get it from the paper if they need it, but they will remember if you can show them why your main result is true from a chain of insights.

Set out as plan for your slides and then discuss with your advisor / supervisor.
They can then suggest changes as necessary and you can then do the next level of detail which can then be checked.
This will be an iterative process, much like your calculations. At the end you should have a good presentation - but it will never be perfect: there will always be one question that needs something else...

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Non-rigorous proof in an article
I am writing about the analysis of a certain mathematical object. The expression for this object is obtainable in several ways:

non-rigorous ways: they amount to just computations
rigorous ways: they are precise and apart from the above computations, one needs to supply some proof of certain passages

I have a fully rigorous proof of the derivation of the expression for this object. I think that including it in my article is no good service for the community, because:

there is no more space
the proof is technical and not enlightening (no new ideas, essentially)

The only element of novelty is that the object is related to a new problem, not found in the literature, but very similar to others. And in a somewhat different formal setting than most other examples, but again, the proof outline and the key formulas/conceptual passages, are already present.
I am targeting a respectable journal where usually, facts are proved rigorously, not formally. And where proofs (formal or not) are not deferred to the supplemental material. That is the space for pictures, code description, implementation details and so on.

Should I include the lengthy proof, hence, in the supplemental material? How about including a non-rigorous proof using a quicker method in the appendix?

Otherwise, is it a good way to go just citing the various computation recipes out there, without spelling the computation (nor a proof) out in detail?

More about "The object"
I am working in optimal control and I have to compute a derivative of a functional. A non-rigorous proof would be to form a Lagrangian and differentiate it formally, without checking that things are actually differentiable, for instance (it is a bit more complicated but this is the essence). The Lagrangian approach is non-rigorous. For a fully rigorous approach one should prove differentiability of every piece and this takes considerably more effort. Say, using the implicit function theorem in function spaces.
The non-rigorous passages are especially already present in the literature, for examples more or less.similar to mine. The rigorous passages maybe are not exactly equal to something seen before, but there are standardized recipes to obtain them (e.g. apply the implicit function theorem).

Perhaps rather than "formal" as an adjective, "heuristic" would be better. In particular, in some mathematical contexts, "formal" means that it's so clear that a computer proof program can verify it. Yes, in the past, sometimes "formal" meant "non-rigorous", but I think by this day it's better to say "heuristic", rather than "formal", due to the drift in what "formal" can mean. :)

Can't you add it in the Appendix?

If you say "proofs are not deferred to supplementary material", does this mean that the journal has a policy to never do that, or does it rather mean that you have looked at a few papers and it doesn't happen there? Because even if generally proofs are in the main paper, it makes some sense to put very lengthy bits in a supplement if those lengthy bits are unoriginal, uninteresting, and not of core importance to the paper. In the paper you can then outline the proof and refer to the supplement.

Sometimes there is a way to write down a proof that treats a new situation but contains many non-original elements in a very short way by referring to other papers wherever possible, omitting details. Often you can get away with this even if a reader who wanted to reconstruct the whole thing would have to put quite some work in. Ask yourself: What is the minimal way to write down how this works so that an expert reader with some time in their hand can follow the recipe, possibly involving cited literature, and convince themselves that the statement holds in this way? A reader who then doesn't succeed doing this can still contact you, and of course a reviewer can complain if they don't find this sufficient, however this kind of thing is not a reason for rejection.
In my experience, quite a bit of proof completing work is left to the interested reader in many math journals, with the effect that proofs can be presented in very limited space if they are not of central importance or interest.
Whether this approach works in your case of course I can't know.
Another option is to put a version with detailed proof on arxiv.

Why isn't the last option (arXiv) the first one?

@user21820 There isn't a ranking in options. These are possibilities and the user who asked the question can use them however they want.

What I meant is that all the hedging about "whether this approach works or not" for the other options becomes unnecessary once the arXiv option is available. It is not just another option, but rather one that appears to be a complete solution. Not enough space? Put the rest in a full version on arXiv and put a link to it in the article to be submitted to the journal. Why even bother to deal with a quandary due to limited space when one has enough space on arXiv?

Moreover, not taking the arXiv option often leads to deliberately omitting proofs even if the technical details are relevant and important. It's just a displeasing state of affairs...

@user21820 Depending on the journal policy and audience it can be important to put so much in the paper itself that the reader (and reviewers) can verify the result, including maybe filling in some straightforward details themselves, without going to arxiv. Of course one can put something detailed on arxiv in any case, but there is something to be said for having a version in the published paper that "works" as a proof even if it doesn't have all details.

Of course, that's good if it can be done. Sometimes, that cannot be done, so the point is that it's important to make the full proof is available somewhere, as the first priority, rather than making 'severe summarizing' the priority. There are still many publication venues that limit the paper to 10 pages even with electronic publication, so after you exclude introduction and background information you have only 5 pages left.

I suggest that you match the standards of the journal if they are clear. Readers of the journal, and reviewers, will look for that and expect it. You will get feedback from reviewers who may ask for changes.
The other option is to write it the way you think it seems best and submit it. Again, the reviewers may want changes.
You also need to consider whether you have chosen the right journal if you think that they way you think it should go isn't a good match. Maybe another journal that doesn't expect complete rigor would be best.

It’s really up to you to decide what is the best use of your time and effort to make the greatest positive contribution to your research community. I’ve also struggled with these sorts of questions and it’s not always an obvious call to make. However, I think your reasoning is influenced by some superficial and irrelevant considerations, particularly “there is no more space”.
If you don’t think the “rigorous proof”* is useful to anyone, fine, don’t write it - that’s a totally valid reason not to write something. But if on the other hand it is actually useful, then presumably there will be a journal that is willing to publish it. Instead of fixating on a specific journal to target and lowering the usefulness of your content to satisfy the journal’s space constraints, consider writing the actual content that would make the greater impact and publishing it in a place where it will be appreciated (either instead of, or in addition to, publishing the slick non-rigorous derivation in the journal you currently have in mind).
* putting this is in quotes because from my point of view it’s a tautology that belongs in the department of redundancy department.

First, this is mathematics, so you really need to include your rigorous proof somewhere in the article.
However, there is absolutely nothing wrong with putting the non-rigorous proof in the body of the article and deferring the rigorous but unilluminating proof to the supplemental material. Supplemental material is intended for things that the average reader of an article may not be interested in, but which may be important for readers who are experts in the subject area. The rigorous proof fits these criteria perfectly.

Writing a paper always means weighing the reader's attention span: you are trying to present enough for your reader to, well, learn something new, without supplying so much information that your reader loses the important details.1 I can think of some possible functional outcomes of not choosing the appropriate depth:

Skepticism: If an important step is glossed over, the reader may find it too dubious and not accept your overall argument.
Brittleness: If an important step is glossed over, and it explains a limitation of your argument, a reader may be tempted to expand your argument beyond its due limits.
Rabbit-holing: If too many trivial steps are expounded, the reader may get lost in trying to prove them and forget the overall argument.
Pigeon-holing: If too many trivial steps are expounded, the reader may think of your result as being very limited (for example due to many things being taken "without loss of generality") and not grasp its general extent.

Surely there are more. I hope you can see that I am encouraging you to consider the functional impact of what you keep in or leave out of a proof, not just whether its form fits a certain brevity or verbosity.
As an example -- I recently published a derivation of an equation, connecting certain thermodynamic ensemble averages, that I've been working on for a while. The equation began life as an equality between some esoteric integrals which I "projected down" into the thing I actually wanted. Later, while writing the paper, I reasoned that there must be a simpler way to prove it; I eventually managed it by shuffling around some integrands, but I was quite unsatisfied because I couldn't see the physical significance of what I'd done.
Eventually, when I published the paper, I only included the simpler proof in the text. But I included the original proof in the supplementary information and wrote a paragraph in the text explaining its physical significance. Alas, the simpler proof did introduce a physically-significant quantity, which I only identified when a collaborator asked me just exactly how it worked (naturally, just after the paper had been published). This is an example of me skipping an expositional step where, had I fussed over writing it down properly, I might have mined an additional insight for the paper.
Maybe you can do something similar, such as writing a shorter proof in your publication and referring the reader to an arXiv document for more details?

1Think of your reader as a biological large language model, and your job is to fit every important concept into the available context window.

Very funny last sentence. It's like you're doing exactly that to the content of your post. =P

"The proof is left as an exercise to the reader" is one of the most irritating concepts in modern acadaemia.
It's the same in other fields where only vague details of methodologies are provided or source code and algorithmic implementations aren't included.
You may think your proof is rigorous, but without including this detail how can a reviewer know?
If it's too long to include in your article, publish it somewhere publicly available (it doesn't really matter where as long as it's not ephemeral), and cite it or include it as an appendix.

Not sure whether this makes reference to my answer, but anyway, there is a fine line here. A reader will want to understand the proof, but may not want to go through lengthy uninteresting bits that they have seen several times before and that they know they could do on the back of an envelope with a bit of time. Obviously a journal paper shouldn't come with "exercises", but still 18 interesting pages can be better than 30 with long boring derivations that a reasonably interested reader could relatively easily reconstruct with some minimal indication.

This is why I suggested publishing it somewhere else that's publicly accessible so those who want to can

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Citing my unpublished master's thesis in the article that builds on top of it
I am writing an article from my master's thesis. It is a polished and much shorter version of it, with equal contents. My master's thesis is unpublished by my university, but available from my GitHub.
I am unsure whether to include some proofs in detail in my article, because too technical and not particularly enlightening. I have received interesting suggestions here. It occurred to me that a different option might be to cite my master thesis for such passages, where they are spelled out in great detail.
I see many advantages:

the thesis is already "peer-reviewed" by my thesis supervisor, a respectable researcher in my area
it is available online
I would make the article more readable, without filling it with too many technicalities, which are however available for the interested reader in the master's thesis
I could include other details and content that would otherwise need to be left out, providing a better service to the community

As disadvantages:

the reviewers of my article may not consider the thesis as a sufficiently valid source
the article would become less self contained (but it is common practice not to repeat things already done elsewhere)
I would be referring to proofs and material which although clear, it is not written and polished with a peer-reviewed publication in mind
the master's thesis uses a different notation

Is it okay and advisable to cite my master's thesis? Are my concerns valid and are there more?

I don't know what the norm is in your field or for the journal(s) you are targeting with your article. However, inasmuch as you say that the article is effectively a version of the thesis, you should consider whether your prior self-publication of the thesis on GitHub presents an issue for publishing the article in a journal.  Journals generally require submissions to be original works of authorship, not previously published elsewhere, and an editor conceivably might decide that your article does not meet that standard.

If your master thesis is publicly available on github, then it is published. Maybe not "published in a research journal", but definitely "published".

@Stef: “Published” in academic settings has a range of meanings, depending on context — “published in a peer-reviewed journal”, “published in any traditional venue [e.g. lightly-edited conference reports]”, “published in any venue that can be expected to remain accessible indefinitely [e.g. major preprint servers]”, “available in any publicly-accessible form [e.g. author’s website]”, …  OP’s thesis is certainly published in the last sense, but certainly not in the first.

@PLL Hello. Yes, the OP's thesis is published. No, the OP's thesis is not published in a peer-reviewed journal. I don't see any ambiguity here. Good day to you.

I am unsure whether to include some proofs in detail in my article, because too technical and not particularly enlightening.

If the results you are proving are original then you should include the proofs, even if they are highly technical and "unenlightening".  For original results the most basic function of a proof is to confirm that the result is definitely true.  This function is necessary even if the proof itself does not assist in illuminating the result.  The usual place for such a proof would be an appendix to the paper.  The main reason you would want the proof to be part of the article is that it is a neccessary part of the demonstration of a result at issue, and a outside source on GitHub could change or be removed in the future.  If the results you are proving are not original then you have more latitude; in this case you could reasonably cite relevant proofs in other sources, including the proofs in your Masters thesis.
From your linked question, it appears that the theorem at issue here is an adaptation of another published theorem, but your version is not a special case of the latter so it is not already proved.  In view of that, I would recommend keeping it as part of your paper.  If you are concerned about the technicality and length of the proof, put it in an appendix instead of the body of the paper.
Finally, since you have just finished your Masters thesis, you should consider going back to your former advisors to get their advice.  They are already familiar with the material at issue and they will be in a good position to give advice on the best place for the proof.

The OP can also publish the thesis on a pre-pint server such as https://arxiv.org/ to ensure that it remains available to everyone in perpetuity. This would remove the problem that "an outside source could be changed or removed". Also in many fields and journals a very summarized style of proof might be allowed or even encouraged. The purpose of most "proofs" in journals is to explain the key insights such that an expert in the field can reproduce them with some work. Not to give a computer verifiable rendition of the proof.

It's also common practice in some fields to publish an extended version of a paper with such proofs on pre-prepint servers if they would exceed the page limits for the paper submission.

It occurred to me that a different option might be to cite my master thesis for such passages, where they are spelled out in great detail.

This can be a good option, and is actually very common especially if you are dealing with a page limit on the present article, or if the present article is focused on something else (e.g. application of the ideas, or summary of their impact), such that the formal development would be a distraction.
However, there is one important caveat: in order to publish and cite the master's thesis, you should put it up via a permanent location such as arXiv or a similar service. A GitHub repository is unfortunately not sufficient for this, as GitHub files can later be moved or deleted.
Addressing your specific points: for the "advantages", I agree with all of them, except:

it is available online

By academic standards, this isn't entirely true for the reasons above -- the thesis may be available online on June 1, 2023, but may not be available in a decade or a 100 years from now unless it is put on arXiv.
Addressing the disadvantages:

the reviewers of my article may not consider the thesis as a sufficiently valid source

This probably isn't a problem; perhaps surprisingly, many good papers cite unpublished or un-peer-reviewed work, including preprints, invited papers, and even personal correspondence.

the article would become less self contained

This is true, but could be an acceptable drawback for your use case.

I would be referring to proofs and material which although clear, it is not written and polished with a peer-reviewed publication in mind

This is also a valid concern.

the master's thesis uses a different notation

This is probably the concern I'd be most worried about. Are you confident about the results you are using? Do they translate correctly to your new setting?
Overall:

Is it okay and advisable to cite my master's thesis?

Yes, it is certainly OK. Whether it is advisable is somewhat of a judgment call, depending on the material. I would encourage you to talk to your masters advisor to get feedback on the present paper structure.

You do not need all the thesis, but simply some proof/results.
Put everything useful from your theis in one or more Appendices to your paper. Eventually, you can cite your thesis in the introduction or wherever needed as

Results obtained by Leonardo (2022) are presented in Appendix A-B-C

One may wonder why cited results are presented again in the appendix, but then when one reads the full citation being a Thesis (unpublished, but usually thesis can be found after enquiring the university library), the reader will be glad they can check the appendixes,
Appendices can be extremely concise, you need no frame nor introduction, simlpy put what is needed.

From the point of view of a reader of your paper, your masters thesis does not yet exist as a peer reviewed publication.

the thesis is already "peer-reviewed" by my thesis supervisor, a respectable researcher in my area

No, it's not; this is not how the peer review process works. For starters, no journal would ask your supervisor to be a reviewer because of close personal/professional connection. And then, accepting a thesis does not mean that it is accepted on publication level. Neither is your supervisor responsible for pointing out issues and making sure they are corrected in the way peer reviewers should.

it is available online

As pointed out by other answers already, GitHub is not good enough for this and arxiv or similar would surely be better.
However, a better option would be that many journals offer to add online supplements to a paper, which will be included in the peer review process. This is a possibility to write a shorter and more readable paper but still to provide the details to the peer review process, and have them accessible online in an "admissible"  place.

the article would become less self contained (but it is common practice not to repeat things already done elsewhere)

As your thesis doesn't count as a publication, if you write a paper for publication based on your thesis, material in your thesis doesn't count as "already done elsewhere".
Final remark: You may want to take into account the general publication culture in your field and in the journals you consider. For example, in (pure) mathematics, often more proof detail is expected than in statistics. You may ask your supervisor about this. Also have a look at how other authors did such things.

Go ahead and reference it.  Jay Earley certainly referenced his
dissertation in his CACM paper; it would be dumb not to.
If you can get your department to house it, that would be preferable
to github.
https://web.archive.org/web/20040708052627/http://www-2.cs.cmu.edu/afs/cs.cmu.edu/project/cmt-55/lti/Courses/711/Class-notes/p94-earley.pdf


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Is it okay to publish your entire work of PhD in low tier?
I am a PhD student works in theoretical computer science(Algebra). I have been working on my PhD project from last five years. I am very much interested in  my work. During my Ph.D there were not collaborator were there other than my research supervisor. I struggle a lot during my Ph.D as problem finding was very tough, solving also and then writing. I even did not find the course work which I did any helpful. I was also not allowed to work outside my university I don't know why. Now at the end of my Ph.D I come to know the value of collaboration.
I have studied most of things in Ph.D. at my own. I come up with results and written those with the help of research supervisor. I have worked very hard in my Ph.D. despite of that I am not publish a single paper in top tier. All of my research paper are in low tier. I will be graduating soon.
According to my research supervisor, PhD is to train a student not to publish something in top tier. This is true for all of his Ph.D students that they publish in low tier.
I am worried about post-doc and Job after my Ph.D as many of the students in my field are publishing at top tiers. I can publish research paper at my own but not in top tier.
Question : Is it okay to publish your entire work of PhD in low tier?

It's unclear what sort of job you want, which makes it difficult to answer this question.

what do you mean by low tier? relatively low impact factors? or  conferences/journals that are basically not peer reviewed at all (e.g. "predatory" open access journals)?

@A Simple Algorithm Low tier mean according to this ranking http://www.conferenceranks.com/visualization/msar2014.html

Just to be clear: Do you want to stay in academia for a long time?

I can feel you bro. I am in the same situation. You are not alone. :-(

Back in the old days, it was quite common for mathematics and theoretical computer science PhD students to graduate with zero publications.  Their research contributions, while valid, were not significant enough to be published.  This isn't so true now, principally because there are many more low-tier conferences and journals to publish low-significance results, so the bar of significance to be published has gone down.
As far as the goals of a PhD are concerned, as long as you have done enough research, it's a valid PhD.
However, the job market is not so friendly.  It's useful here to bring out the sports analogy.  Getting a permanent academic job is like getting to play on a major league baseball team (or a first division football team).  Getting a PhD is like becoming competent in a minor league (or lower division) team.  Not everyone who starts out playing professional baseball (or football) makes it to the top, and you need talent and luck as well as hard work.
Most people who finish a PhD don't have the right combination of talent and luck to land a permanent academic job, just because there are fewer jobs than people with PhDs.
In the current job market, in order to land a permanent academic job where research is a significant portion of your duties, you need research results that can be published in a higher-tier venue.  If you don't get them as a grad student, you might get them as a postdoc, and it even happens that people get them doing research nights and weekends while working at a non-academic job, or a teaching-only academic job.
But, just as the sports analogy suggests, while there are things you can do that will help your chances of making it to the major leagues, there is nothing you can do that will guarantee (or even make it highly probable) you make it to the majors.

I am not interested in joining industry despite of that I will join some college.

Back in the old days, it was quite common for mathematics and theoretical computer science PhD students to graduate with zero publications. — The old days must be really old.  When I got my PhD in theoretical computer science in 1996, finishing a PhD in theoretical computer science with zero publications was already rare, and getting a faculty position in theoretical computer science with zero publications was already impossible. — the bar of significance to be published has gone down — I don't think this is true at all; fruit was much closer to the ground in the Old Days.

First, I'm not sure where to draw the line between top and low tier journals. You want to publish in an appropriate journal at the higher rather than the lower level.
But it is more important to realize that your career doesn't begin and end with your doctoral research. It is normally only the first of your published works, not the best, and certainly not the totality.
Some people are lucky in their studies, having been given a hard problem and having made significant progress on it. Others have done more modest work. But, there is actually more valid doctoral research than the top tier journals could possibly publish.
So, it isn't something to worry about. But seek out interesting problems and work hard to solve them. Get as much published as you can and in the best journals you can manage. Your career will grow. It doesn't start out fully formed.

This does not answer the question.

OP is a theoretical computer scientist, so replace "journal" with "conference" everywhere.

@AnonymousPhysicist: This does answer the question.

Actually, there is a flag for posts that don't answer questions. The mods will intervene if they so judge.

I am worried about post-doc and Job after my Ph.D
Question : Is it okay to publish your entire work of PhD in low tier?

Yes, it is okay. As you are nearing completion, you need publications to get hired. If the alternative to publishing in a lower tier is not publishing at all, then you are far better off getting something in print in a good peer-reviewed journal with a respectable impact factor, even if it is not your first choice.
The harder question is how much of your doctoral work needs to get published at this stage. You can publish some of it while saving some to rework, polish, and submit later, with better hope for an outstanding publication. Ask your research supervisor for their advice on how much is enough.
That said, I strongly agree with @Buffy's advice, which I up-voted.


text:
A PhD thesis without any publication
I am currently a Ph.D student(computational maths) works in a theory. I will be graduating in the next year. I have one paper which I will be submitting soon and working one more paper. One of my research article has been published but not related to Ph.D thesis. My first research paper is fully reviewed by my advisor several times. I don't know I will be able to publish anything more in my Ph.D as this is my second last year. I have put of lot of effort in my Ph.D my supervisor also have admit this thing, but verbally. I don't want to do go for a faculty job after my Ph.D, I will be going searching a post-doc after my Ph.D. I am worried about whether I will get a post-doc or not. According to institution norm's there is no requirement of publication in Ph.D.
Question : Is it going to harm my research carrier if I submit my  PhD thesis without any publication?

Which field is this? Are you planning to publish your PhD thesis as a book? Or parts of it as articles, after graduation?

Have you discussed this with your advisor? If so, what did she/he say? If not, why not?

I disagree that this was closed. It seems to me to be perfectly suited to this site and useful to future visitors. The question is objective and readers here probably have experience to offer guidance.

@Buffy You can vote to reopen. I did. My impression is that sometimes questions are closed prematurely by people who can't imagine a generally applicable answer.

This sort of thing varies by field. In some, there is no expectation at all of publications prior to finishing the degree. I think the push toward requiring publications is somewhat recent. When I finished (long ago) in mathematics it would be very rare to have any publications at all upon graduation.
But in some fields there is such an expectation. However, I think that in those fields, students are funded more for research (RA) than for teaching (TA). If you are part of an active research lab in the sciences it is more natural to have several publications as a consequence of your work prior to graduation.
But any effect at all on your career would likely be very brief. You establish your own reputation. Starting a bit late with publications eventually evens out if you are productive, either in academia or elsewhere.
Of course, it won't harm you to be thinking about what you could get out there in your time remaining. Your advisor should be able to tell you about norms in your field, of course.


text:
A professional reference letter for pure math graduate school
I'm applying for master's degree in mathematics (pure math) at Canadian universities.
I already found two professors to write academic letters for me, but it's hard to find the third one who can write a strong letter.
All schools mentioned on their websites that they require 3 letters with at least two academical references which means the third one could be professional.
I've been working as a math tutor at a community college  in Toronto for past 3 co-op terms. She has supervised me for 2 co-op terms and knows me very well (even more than my professors).
Her position is Learning strategists - math specialist which means her job is to support students' learning and deal with their academic concerns. Before the current job, she earned her master's degree in mathematics and statistics and worked as a lecturer/teaching assistant at a university for 5-7 years and was an instructor at the current college for few years. I don't want to reveal too much about her, but at least I can say she went to/worked at top Canadian universities.
I have built good relationship with her as a co-op student & supervisor and I have some impressive achievements in a college tutor level. So I believe she can write a strong letter for me.
My concern is she doesn't hold PhD. Would committee take her letter seriously? Do you recommend to get a letter from her rather than from a professor who barely knows me?

That is of course always hard to answer, as we don't know you, we don't know what would be written in the letters, we don't know about the person reading your letters. Thus, the answer below is just my personal opinion, it might or might not align with the opinion of the persons in charge of admitting you:
I would go with the letter from your job. Your job is math related, the person writing the letter is working with math daily and she knows you better than the third professor. Thus, you would get a personalized letter instead of the generic "Andrew is a good student and passed my class with an A" that admission boards surely read way too often. Furthermore, it shows that you really enjoy math and not just study it to get a degree. With the right wording, this could show you as a really motivated mathematician; and every professor knows that to do a master's or maybe even a PhD in pure math you need tons of (self)motivation.
I wouldn't worry too much about the fact that she doesn't hold a PhD. On the contrary, she has been allowed to work and lecture at top universities without having one, that tells way more about her than a piece of paper saying that she wrote a thesis at some point in her life.
Oh, and if she already worked at top universities, maybe she also worked at the one you are applying to and has connections there? That would put her letter even above the two from your professors I'd guess.

At least my supervisor said she would be happy to write letters for me. I will see how it goes. Thanks!

I don't see this as a concern, given that you are applying for a masters program and not a Ph.D. program. In fact, if you intend to teach when you have completed your masters degree, and especially if you plan to (or hope to) teach as part of your assistantship (or whatever your graduate support money is called), then she could actually be your most significant reference.

Thanks for your advice. I was wondering how much ppl in the field of pure math care about teaching & facilitation cause I always thought high research skills are what they are looking for from students first.


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Code plagiarism by teacher at renowned university
As a post-graduate student at a renowned university, I am supposed to make an assignment (see attached images) which is obviously inspired on this licensed scikit tutorial.
Since the assignment (code) instructions are identical to the licensed code, I have two questions:

Is the scientific integrity of the teacher challenged by posing this question?
Should I report this at the university's fraud office?

In the assignment is no reference or citation included.

Plagiarism means claiming credit for others' work as your own.  Is your professor actually claiming this work as their own?

Before you step into a potential minefield of accusations and possible blowback, I'd suggest that you just discuss it with the professor, raising your concerns about citation. A fraud accusation would be very serious and possibly unwarranted. You don't know whether the professor has discussed this with the team that created it. Also their own materials only ask for citation if you "use it in a scientific publication". The funding agencies (INRIA, for example), may require fairly loose restrictions on use. I didn't investigate the BSD license, so it may be restrictive or not.
But delay serious steps from which it would be difficult to extract yourself until you know more.
I'm sure many people have turned some of my work into student exercises (not published outside the course material). I would, myself, never object to that.

The BSD license is, perhaps famously, not restrictive at all.

IMHO, this is not a scientific paper where there is new contribution he is claiming. Academics have enormous and diverse set of tasks more than you imagine. It can be unintentionally ignored or oversight. It can be that he is acknowledging it but not to the students to not search for solutions online.
Therefore, I advise you to assume a good faith and talk to him personally in a friendly way to point this to him. Especially if solutions can be found online.

for what I can find the scikit tutorial are under the BSD licenses and from what I can read from the homework's description  nothing is violating the terms of service.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

https://en.wikipedia.org/wiki/BSD_licenses
https://scikit-learn.org/stable/documentation.html
https://opensource.org/licenses/BSD-3-Clause

Maybe?  Not really.  I don't think anyone cares.
I would advise against reporting this to anyone.

Explanations:
1.) This isn't a peer-reviewed paper; it's a homework assignment.  It's also an assignment in a field that isn't well supported by years and years of instructional material, like textbooks, etc.  So It's hard for instructors to come up with good assignments.  If your instructor had taken a problem out of a textbook and given it to you, would that ping your suspicions?  (I can hear someone arguing: "But wait! If it was from a textbook, I would know it wasn't his own work, and I wouldn't be suspicious."  To which, I would reply: "Sure; see previous point about not much in the way of established instructional material.  Also, if your instructor had given the class a citation, it might have included solutions.)
2.) If this was in a book published by your instructor (and I don't mean a fancy set of handouts, I mean published), maybe someone would be upset.  Perhaps the original author.  If you bring this to the higher ups in the university, I could see more potential difficulties for yourself than for your instructor.
Summary:
Is this the "best" instructional practice?  No.  Is this commonly held to be "OK" instructional practice?  I think you will find, yes, it is.


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Is it possible to make minor (making a space between two words) proof corrections after already submitting a proof reading to a journal?
After submitting back an online proof reading corrections of an accepted paper, I found a very trivial mistake; just making space between two words. The words take vague meaning if left not spaced. Is that possible to make one more proof read to correct this typo error?

Does "an online proof reading corrections of an accepted paper" mean "camera-ready version"? If so, then you need to act immediately, since the publisher may be near ready to release on an online version, and I wouldn't expect the publisher to permit changes at this stage. (Camera-ready is final.)

Thanks all. But I noticed the error after the article was released online (published).

You can try to correct it by contacting the journal. they are the only ones who can decide if they want to change it. On the other hand: nobody cares about the extra space (like it or not). We are interested in the science.

Thank you Louic. I'll try to contact the journal but I'm afraid if they release the article as "Erratum" or "Corrigendum" because of this very minor mistake. To explain the problem it is like "late aged adult" and the error happened when I write it as "Lateaged adults". Mind the space between "late" and "Aged". This error happened in 9 places in the paper. That was the problem that I notice after the paper was published.

The journals I'm familiar with reserve errata for significant errors, which this is not. They may say "oh well, this is how it is now", or make a slight adjustment given how recently it was published.

Email the production editor as soon as possible that you've found this extra correction. If it's still not inconvenient for them, they'll probably fix it. However, because it's such a minor error, you should be ready for them to say "it's too late" as well. This probably won't lead to an errata or corrigendum - it's just too minor.
If your previous reading had contained lots and lots of corrections, it's possible they're already planning to send you a set of second proofs.

Thank you all for the explanations and important ideas. Unfortunately the paper was published online two days ago, and I identified this very minor error after one day of the publication. This "lageaged" consistently occurred in many places that increased my worry. After looking at most of your suggestions, I emailed the production team to ask about this and now waiting for their response.

If it's already been published online, chances are it's too late.


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Asking research committee about on-campus interview
I had an on-campus interview for a tenure track position last week in the US. The department chair told me that the results should be available within week. By today, a week is passed away. Is it ok to contact the department chair to ask her about the interview results and If I was selected to get a job offer or not?

What country was the interview in?  What exactly do you mean by "last day of this interview-result notice." ?

I mean by today, a week is passed away

I would wait for a few more days, actually. You don't want to seem too eager. If you are high on the list, you may still need to negotiate a few things, and it is better to be a bit calm about it. Let them come to you.
It is what it is, of course.
But if you have other decisions to make immediately, then you may need to ask now. Otherwise, patience is suggested.


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Dissertation: How to properly reference earlier versions of working papers in the German academic system?
I recently became the co-author of a working paper an older version of which is online (at which stage I was not a co-author yet).
We added and changed most of the content, however some applications remained virtually unchanged. How do I need to cite/reference the earlier version of this paper to avoid plagiarism concerns? We already added "An earlier version of this paper circulated as old paper name".
I do my PhD in Germany. How do I need to cite/reference the old working paper to avoid any plagiarism concerns?
Based on the comments:

The earlier version of the paper was not pubslished in a book/journal, but posted online on SSRN.
I am not worried about how journals perceive an evantual submission, but merely about the (german) academic regulation(s) regarding plagiarism.

If it was a working paper that never appeared a journal or conference proceedings, you are entirely within your rights to submit it anywhere you want. And it doesn't really matter how you reference it the original; just follow the journal's style guide as closely as you can.

What I typically did in such a case was either a footnote at the title in the gist of

A previous version of this paper appeared at XYZ Conference in 1201.

or a mention in the introduction with the citation

This paper is based on our previous work [ABCD+ '01].

Two side notes:

If this is a paper and you submit double-blindly, you'd need to revise the statements accordingly. You might even want to remove them for review and/or inform the editor.
The information on previous versions and an explanation "what's new" belongs into the cover letter of a journal submission.

As of now, I am mostly concerned with the german academic regulations. With many people losing their degrees for "academic malpractice" (for lack of a better term), I want to make sure that in the submitted thesis, all referencing is done properly.

How do I need to cite/reference the earlier version of this paper to avoid plagiarism concerns?

From what the OP has written, I cannot see reason for plagiarism concerns. Releasing an early draft of a paper (even with different authors and a different title) and subsequently releasing an extended version does not constitute plagiarism. Nonetheless, it is useful to note that an earlier draft exists and that draft can be cited in the usual way. (With arXiv, and probably other such services, you can use a distinct identifier for each earlier version.)
Going beyond what the OP has written, plagiarism concerns exist if: an early draft was published, rather than merely publicly released (e.g., as a technical report). In this case the most recent version can only be published under certain circumstances, e.g., in some disciplines, as a journal article that follows a conference paper. For PhD students, another plagiarism concern might be the inclusion of material from the earlier version in their thesis. This should be addressed in the same way as any work that a student has not produced themselves and should be explained in accordance with institutional guidelines, which may require a section devoted to explaining what the student's contributions are, for instance.
Other plagiarism scenarios may exist, but I cannot identify them from what the OP has written.

Second paragraph: this isn't plagiarised work, it's just no longer original work.

@henning Claiming the new version is original when an early version has been published is surely self-plagiarism?
(Also, claiming work by a co-author is that of a PhD candidate is clearly plagiarism. But, I presume you're referring to the former aspect.)

Yes, I was referring to the first case. Plagiarism is passing of someone else's work as your own. Hence, "self-plagiarism" is an oxymoron. I know, this IMO nonsensical term is sometimes used, but at least it should be clear that "self-plagiarism" and plagiarism are very different animals. Most researchers work on extensions of their earlier work, and although it's a good idea to reference own preceding work, failing to do so is not a grave misconduct, unlike plagiarism. Also, what counts as "least publishable increment" differs strongly between publishing venues and disciplines.

@henning I largely agree, but, plagiarism has been defined (by some) to include self-plagiarism, so it seems prudent to mention self-plagiarism to the OP. Regarding "failing to [cite earlier versions] is not a grave misconduct," that depends whether such versions were published, rather than publicly released, duplicate publication (https://en.wikipedia.org/wiki/Duplicate_publication) is misconduct, albeit, less so than plagiarism.


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Citing draft papers
I'm working on a project where I've come across a couple relevant papers that are marked as "preliminary drafts" and/or with a request not to cite them because they are preliminary.
Should I cite the most similar, published work, ask the authors for their preference as close to publication as possible, or take a different route?

The answer to this question depends upon the specific journal you are submitting to and the authors' preference. For example, the Journal of Applied has a specific policy described here.

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


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Legal protection for the title "university" in California
Some non-academic organizations in United States use "university" as part of their name without official accreditation, and I've been struggling to figure out to what extent the university title is protected in the U.S. I'm particularly interested in California law.
In New York State, EDN § 224 prohibits non-accredited organizations from referring to themselves as a "university," but I haven't been able to find similar federal or California regulation.

I'm voting to close this question as off-topic because it is better suited for Law SE.

@user3209815 that's not a valid close reason. If it is on-topic here, it stays, even if it wouls be more on-topic elsewhere. Some animals are more equal than other animals, Oceania has always been at war with Eastasia.

According to wikipedia there are no national level protections in the USA, and California "permits anyone to claim to operate a college and issue degrees with essentially no oversight". Given that they're so lax in that respect, I'd speculate that they're unlikely to have protections for those terms.

Unlike some other countries, there is no strong federal regulation that controls the titles like "University" and "College".  A few states have state level regulations, but federally there isn't any.
By the looking at the number of degree factories in California, I doubt that state of California has strong control over the title as well.
Some people became professors in regular four year colleges outside of the states with PhD's from these colleges without attending the class once or even visiting the campus - well, there isn't any campus to visit anyway.

I am sorry to say this, but any university that lets someone become a professor based on a false degree, deserves said applicant.

Yes, it is really pathetic.  Even in the states, it is a real problem.  There should be stronger regulations.  It really sickens me.


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Repeating a proof from the literature in my paper
This question is about writing a paper in mathematics.
I am studying a (partial differential) equation and an algorithm to solve it approximately (finite element method). I need to report in my work a theorem on the approximation error of this algorithm. Such theorem already exists in the paper X: it is proved in a context that is more general than mine for some reasons (moving vs non-moving domain), and slightly less general than mine for other reasons (homogeneous vs non-homogeneous boundary conditions).

Should I report the adapted version of the proof from paper X, after of course appropriately citing it?

The modifications I had to do to the existing proof are mostly "trivial": my estimations are just longer and slightly more technically involved versions of those in X. In one point, however, I make a non-trivial (not so ingenious either) conceptual passage. I need a lot of context to report and prove this conceptual passage, so that rewriting the whole proof in my paper is not so much additional work, and it would be of course clearer.
Long story short, reporting the whole proof seems pedantic and may not be well received from the reviewers, whereas saying "The proof is as in [X]." feels lazy or not informative enough to me. But there may be more leftover space for reporting original content directly related to my publication!
Any hints?

I think there’s no way to guess what a given reviewer might find preferable in such a situation. If you put the proof in, a reviewer might ask you to take it out, and if you leave it out they might ask you to add it. (And if there is more than one reviewer, they might disagree with each other.) So, probably it’s best to just do what you feel would make for the best paper that best serves the community of people interested in the topic of the paper.

If you're a student, you should ask your advisor.  There's not a right or wrong answer, and your advisor will be better equipped to give you guidance than someone on the internet who only has the information you've provided here.

A pertinent question is: how long is the proof? I have done both things depending on the length of the proof. If it is less than half a page, adding in the adapted proof (explaining it needs to be slightly adapted to the situation) should be fine. If it's longer, it's probably best not to, and just state what modifications need to be made to the proof (if they really are easy modifications).

Your concern about it being pedantic and not well received is unfounded. It is a healthy attitude that since their result does not cover the case you need, you consider it your (unfortunate) duty to give a proof. It may be pedantic, but pedantic in a good way, nobody should reproach you for it.
In my opinion, "the proof is as in X" should be considered an option only if the proof is verbatim as in X. Even then, it's better to acknowledge something like "the result in X formally does not apply to our case, but the proof transfers verbatim." If the proof is applies mutatis mutandis, write "the proof works verbatim once one replaces all derivatives with finite differences." In other words, it is an option to describe a proof in a "perturbative way" - by referring to an existing proof in the literature and describing what has to be changed. But at some point it may get awkward, and it becomes cleaner to give a self-contained exposition. It's your call as an author.
It's good, of course, if the role of the proof is properly explained: "We follow closely [1], with modification that may be obvious for an experienced reader. Nevertheless, because (reasons), we chose to include the proof." Relegating the proof to appendix, as suggested, is also a good way to signal your view of its originality.
If you  submit to a journal with a page limit and have to cut out the proof, it would be a service to the community to keep a longer version publicly available on arXiv or your webpage.

+1 I think think it's worthwhile to stress again that the suggestion in the last paragraph (at least keep the proof in the appendix for the arXiv version) is particularly good. Mathematics is too full of folklore results that have never been properly written down by anybody because "it's a simple modification of XYZ" or "it's only a combination of well-known arguments" - where "simple" and "well-known" actually means "simple and well-known to those who have been working in the field for many years".


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Contraints for an article
I'd like to write a scientific article from my master's thesis.
My supervisor offered to collaborate on this, and become co-author. I would answer positively if it wasn't for the following considerations:

he wants to target journals of a certain level, and I don't think my work is up to these standards (yet?)
this is mostly because of two weak points in the actual content of my work. Improving these two weak spots will require a very significant effort: doing new research, learning new topics, writing more arguments...
I would like this article to be published quickly, to take advantage from it in my early career life. The journals of my supervisor take many months (sometimes a year) to have the work published. This is incompatible with my timeline
and sincerely I am okay with the work as is, with its weaknesses. I don't want to put new research effort into it.

I'm not entirely sure what his opinion on it is, on the two weak points for instance. I know that he thinks it's suitable for a publication. I also don't know in advance what his specific plans for the paper are (only shortening and rewriting? Adding more content? Fixing the weak spots?).
I would therefore like to ask for a meeting, and tell him about my concerns, before confirming I want him to work with me on the paper. In particular that I don't want to put the effort required to fix the two major issues, and something about my timeline. And gather his opinion on those issues too. Maybe they're not such a problem as I imagine.
As for me I am working full time, and I'm not in academia anymore. But I might return there. I'd be writing this paper during weekday evenings.
Is this something sensible to tell my supervisor?

Is it correct to say you're not in academia anymore and don't plan to return?

Yes, talk to your advisor. Maybe they want to spend the time shoring up the weak points. You say you haven't had much feedback - now you need some.

@BryanKrausen I am deciding whether to apply or not for a PhD. If so, I will send applications within few months. And no, now I'm not in Academia.

How reliable is your knowledge that you can "publish quickly" in certain journals and that those suggested by your supervisor take ages? It may depend on the field, but personally I'd think that journals that can guarantee to publish work with serious weaknesses (I'm not saying that this is so in your case, but you are apparently assuming it is) quickly are journals who are seen as low level/predatory for a reason, and if you return to academia at some point, a publication in a better journal may count much more for you.

In my view there is much "random" variation in how long the peer review process takes (and by the way also in its outcome), and this can mean that you'll have to wait for long even at certain low level journals, and on the other hand things can go quickly, at least occasionally, at a higher level.

Unless there's a good reason, you don't always need a timeline. Sometimes good work takes time- for real.
And... believe in yourself. I know it's cliche, but it's true. Current paper I'm working on uses tensor math- I remember texting my coworker "we should stay away from the tensor, I'm not good at it". But, now I'm glad I didn't listen to myself. I've learned SO MUCH more than I otherwise would've if I didn't have the courage (I guess) to be uncomfortable and learn new concepts or ideas. And we're not even done with it yet, I still have more to learn. Is it scary? Yeah kinda. But it's also good that I have the opportunity to learn new methods and things in my field.
You don't need to do this by yourself. It isn't just you writing the paper. If your coauthor has high standards, don't shy away from them, set yourself up to meet them. That's the thing about collaborating- even if your work may not be up to those standards right now, they'll be MUCH better by the time you've finished your paper for a top tier journal.
Full disclosure: I'm a phd student, so research is kinda my life, so don't take my view as gospel. But, that's what I would do. Either way, consistently meet with your coauthors in general. That way everyone's clear about expectations and we can voice our concerns like that.

You should express your concerns to your advisor as you have stated them here. There shouldn't be any issue about that.
But you should also, probably, defer to them on a decision to publish or not and take guidance on what still needs to be done. They almost certainly have sufficient experience to judge the quality of your work.
I fear you are exhibiting imposter syndrome a bit in your question.


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Someone copied and submitted my code as theirs, what should I do?
My firend submitted my code on his assignment without my permission and said if something happens he will take the blame, what should I do now ? I am very stressful

You've already asked this question here.

You cannot be certain that he will take the blame. Furthermore, even if he takes the blame: You may still be in trouble if the administration is of the opinion that you should have spoken up right away.
Many on this site will suggest you report this friend immediately. This is probably the safest course of action. This does however burn your friendship with this person. (I'll leave up to you whether you want to be friends with someone who submits your work without your permission.)
IN THE VERY LEAST, if you do not do anything else: document everything. Save the emails where you sent him your code, save the chat conversations of him asking for it, etc. etc.
P.S. If you don't have such emails/conversations in digital format, you could bait them into making an admission of guilt: send a casual message to them along the lines of "About my code you submitted for assignment XXX, I don't appreciate it and I'm worried it will be found out. What will we do if you are found out?"

If the one who is taking the blame that he submitted without my permission then how I will be in trouble? Could you please explain this point

@WaleedNoon Both sharing your code/giving answers to another student and submitting someone else's work as your own are likely against the rules. Whatever "blame" they take, you're still responsible. Why did you give them your code?

I didn’t give him my code but am not sure how he got it

Am I still in danger as I didn’t share my code to him and he was my firend I think he took picture while I was working and I didn’t sense . I tried my best to protect the and secondly, there is huge difference in my and his report his report is poor quality but in mine I explain everything. I submitted on deadline day but he applied for extension and submitted after 10 days

@Sadstudent I think your instructor will find that story difficult to believe, but in any case, since you are now aware of the situation they could certainly find you responsible for not reporting it.


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Are my expectations unprofessional about my graduate advisor?
I am in my first year of MSc program and I have some concerns and I would appreciate it if you could let me know whether these expectations are unreasonable.
Before I start my work with my advisor, we agreed on a project and on the courses I have to take. When I started my work with my advisor, he asked me to work on a completely different thesis in a different area of research and he asked me to drop my courses and take them next year. Meanwhile, I have been getting yelled at even in our early meetings with personal criticism. Also, asking questions of him is quite scary and usually does not lead to an answer but more criticism. However, he always responds to emails very fast and he is always on time with his meetings which are good things about him. I do not know how common these behaviors are, what parts of it is reasonable to continue with, and I do not know if I have to rise any of these issues with the department or I should take whatever that is happening.
Thank you for your help. I am in early stage of my academic career and I am really confused.

I think it's hard to answer: "personal criticism" might be valid (e.g., hypothetically, if you promised to read some papers but didn't), reasons to change the project and drop (change?) the courses might be valid (e.g. if the question in the original project was solved, or if they found an objectively 10x more exciting project (although I would certainly ask why they decided to change the project)). One question you can ask yourself is whether you would be happy to work with this person. Spending 2 (or more?) years in an atmosphere you don't like at all might affect your mental health.

When I started my work with my advisor, he asked me to work on a completely different thesis in a different area of research and he asked me to drop my courses and take them next year.

Why would he do such a thing? If he can give you an explanation that makes sense and that is aligned with your goals, then maybe there is no issue. But I suspect he is doing this because he urgently needs help on this other project. This is a red flag for two reasons: (1) he is making this decision unilaterally and with little apparent regard for your goals, and (2) he probably greatly overestimates how much help a first-year master's student is able to provide, which will lead to problems.

Meanwhile, I have been getting yelled at even in our early meetings with personal criticism. Also, asking questions of him is quite scary and usually does not lead to an answer but more criticism.

I suspect this is a good example of the "problems" I predicted above. Of course, it's hard to judge from afar, maybe he has good reason to be frustrated with you. But either way, talking to your advisor should not normally be "quite scary."

what parts of it is reasonable to continue with, and I do not know if I have to rise any of these issues with the department or I should take whatever that is happening

What are your other options? It sounds like your concerns are probably legitimate and it would be reasonable to switch to another advisor. If you can do so easily, great. But if finding another advisor will mean leaving the program, applying somewhere else, and starting over, then it's hard to say....sometimes it's better to cut your losses, other times it's better to tough it out. Probably something only you can decide. If there's someone in the department who you trust, someone who knows both you and the advisor, then maybe approaching them privately for advice is a good next step.


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Software engineer vs research associate in not-so-related subfield for CS PhD
I currently have 2 job offers: high-paying software engineer at a top tech company (return offer from internship) and a computational biology research associate 2-year pre-grad school position.
I want to pursue theoretical CS (mainly computational complexity, maybe approximation algorithms) so I don't know how much weight the comp. bio research job would carry. The research job also pays less than half of what I would be making at the software engineering company. I would much prefer the comp. bio job since it is at a very innovative non-profit company and the PI and I click super well. I am also really passionate about their mission and the work that they're doing and I'd love to be a part of it.
However, the pay is far worse and I would have to work there for at least 2 years as opposed to the software engineer job which I could quit after 1 year and apply to grad schools during that 1 year.
So I'm wondering, despite which job I would enjoy more, which is the more logical choice? Would either of these add to my PhD application at all?

Lots of trade-offs. I don't think either of these is necessarily better than the other for later admission for theoretical CS. Money is good. Research is good. Quicker entry may be good, though that depends on many other things.
In a situation like that, I'd guess that "follow your heart" is probably best. You don't seem to suggest that the money is driving you - which is a good attitude for an academic.
Either would add something, but neither would be determinative, IMO.

I'm going to second the "follow your heart" approach. Yes, it can be hard to say no to the greater amount of money, but I'll point out that it may be that much harder to decide to enroll in grad school once you change your lifestyle because of the higher income. Research experience (of any sort) is a plus to your PhD application and I've known many people who were unhappy with a high pay position but just stuck it out for the salary, often longer than was mentally healthy for them.


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Research supervisor gives me no freedom-- controls all aspects of my research. Feel like a research secretary. Is this normal in academia?
I'm currently working in a computational research lab where my supervisor just hands tasks to me to do that will help him with his papers but I don't get any input in the creative process whatsoever. For example, he's asked me to transfer data and create data tables but I'm never given any context for the project scope or involved in the planning or exploratory/research process, just in the execution. When a postdoc or somebody from another research group asks for his help with a random tech-related task, like debugging some computer issue, he hands it to me instead. I've been in this lab for half a year now and have nothing meaningful to show for it, besides scattered pieces of code written here and there and essentially serving as tech support for people.
I asked for the chance to lead a project and he assigned me one, but he said that he'll be assigning me the tasks which will eventually converge to a paper. I'm not given any context or "big picture" questions or allowed to take my own approach to answer them. He essentially has a list of pipelines he wants me to run and just output the results for. I feel like I'm just getting assigned busy work and not allowed to contribute my unique background/skills.
When I've been done with all my work, I've tried taking simple tasks and making them into a larger-scale project/applying more CS concepts to them but he disapproves and says it isn't priority and hands me more random tasks instead.
He has given me tasks to do late in the evening to have done by the next morning. I asked him to give me more advanced notice going forward to which he essentially responded "People in academia love their research so much that they don't mind putting in extra hours. If you're not willing to work after hours then maybe you're not cut out for academia."
I am totally used to and enjoy working long hours on research projects, and have done so without hesitation in past research experiences during undergrad because I had a sense of ownership over my work and freedom to be creative with it, but here I'm just working for my boss to help make his name bigger. I'm not getting authorship for my work or allowed to pursue long-term meaningful projects. I could be working as a software eng. making muuchhh more than what I'm earning (turned down lucrative job offer) but I chose this because I enjoyed the freedom and creativity involved in my past research much more than being handed random dev. tasks to make money for some for-profit corporation. But this doesn't feel very different from that aside from the huge paycut and having to take work home.
He also doesn't allow me to attend workshops/conferences at the institution I'm at. Every time I've asked to attend something that interests me he says "this other task is a bigger priority" or "that's irrelevant for the task you're working on" even though I'm really interested in exploring what other people are working on and networking.
So overall I feel a bit more like a secretary and less like a valuable member of a research team. Is this what all research is like in academia? If so, I'm concerned this may in fact be the wrong path for me. Any input/advice is very much appreciated.
Update I ended up switching to another lab and my experience is significantly better here. Some of the other researchers in my previous lab that I wrote about opened up to me about their experience there and it seems like the culture in general was pretty toxic (most of us have since moved on to new labs). Thanks everyone for all of your input-- it really helped me reach this decision!

Are you a doctoral student in the first year of study? What country?

Personally, I would wait for some of the more "well known" contributors to "weigh in" before attaching any weight to some of the comments...

No, research in academia (and indeed out in industry) is usually nothing like this. It sounds like you have a bad supervisor - it happens sometimes unfortunately. Maybe see if you can move to a different group.

I'm not a doctoral student, I'm a research associate at a research lab affiliated with a university in the US (I don't want to give too many details for the sake of anonymity). I'm applying to PhD programs next fall which my supervisor is aware of and is one of the conditions of the job. Hence, I'm curious if I can expect research to be like this during my PhD years (and beyond) as well.

Does your current advisor have any PhD students? If so, how are they treated?

You know this horror movie? It gives good advice in its title: "Get Out!" - get another supervisor, this is not how a researcher should be treated. Giving a student a lot of work and, initially possibly little initiative may be ok in a competitive group, not giving them the big picture is not. Even so, students differ in how much initiative they want - and if you want more, pick a different group.

I'm not a doctoral student, I'm a research associate at a research lab affiliated with a university in the US

So if I'm reading that right, you are not a student. You have completed your BS degree and you are an employee (if that is not correct, please clarify the question). The PI in the lab is not your advisor, he is your boss. So your boss is treating you like an employee, and not like a student. You should not be surprised by this.  You are an employee and a fairly junior one at that. If there is any mundane task to be done, it's going to come to you.  You will find that the experience of being a graduate student is very different than your current position. You will have considerably more ownership / freedom on the direction of your research (not total control, but much more), and you will definitely get authorship credit for your work.
Having said that, there is also considerable variation from lab to lab and from professor to professor in their style of working. Some professors will try to give even undergraduates a meaningful research experience, but others might treat even experienced doctoral students in the manner you have described.  You may have just ended up in a bad lab. When you are applying to graduate school, when you go to visit the campus, the most important question to ask the professors is: "Who are your graduate students and where can I find them?"  Then go ask those graduate students what it is like to work in that lab with that professor.  If you don't like their answers, then you know not to work in that lab.

Also, because of the plan to apply to PhD programs, the OP is not likely to stay for more than a year. That reduces motivation to have the OP invest time in getting the big picture. On the other hand, assigning tasks late at night and expecting them to be done by morning is not proper treatment of anyone, unless it is a very unusual emergency.

@PatriciaShanahan, wholy agree.

Even if they’re just an employee rather than a student, this isn’t a very good way to treat them, especially in IT. The number one question employers are likely to have about his experience there are “what did you do there?”

@nick012000 This is my precisely my concern. I'll be applying to PhD programs next fall so I'm worried that my lack of meaningful research experience during a research position will reflect poorly on my ability to be a successful graduate student.

@mayradio0508, I don't think you need to worry about this.  The majority of people applying to graduate programs have absolutely zero research experience.  Any experience whatsoever, even a non "meaningful" one, will put you way ahead of the game.

I got the same experience just like you. Remind that the research should be observed then discussed comprehensively. Therefore, we have to consider whole factores and knowledges which should be included inside the research we purposed. Thinking positively, it will improve our knowledge and skill better on the research field we concerned. However, it needs more works to do all of that. Having consult with your supervisor and experts on it help you for more,  at least you seems more active and progressive on your work. Good luck for that.


text:
For graduate school applications, is it worth retaking classes with poor performance or just focusing on future class marks?
So, I am a physics student at UC Berkeley. However, at one point, just due to its utility and my own passion for the subject, I wanted to double major in math. Around a year ago, I had very bad personal circumstances which led to notably poor marks in two of the three courses I took that semester, namely two C+ marks. One of these was in an upper division math course, which, today I feel good about in terms of how I understand it, given that I use it almost daily. Due to this fact, I wonder if I should retake this course for the sake of graduate school applications. This question also extends to other courses I haven’t performed that well in.
As of now, my cumulative GPA is a 3.0 (have been receiving B- or B in most technical courses, unfortunately), which almost says no to any graduate school (especially because at the moment, research experience simply is not enough to compensate). This is largely a result of the fact that I have immense exam stress, rather than the fact that I don’t understand my courses, but of course graduate schools would not care about this or see this just by seeing my GPA. I have calculated that if I were to receive the A mark in the remainder of my courses up until graduation, I could end with a 3.7. However, that could be higher if a retook a course or two, one of which is that upper division math course. But would graduate admission officers really consider a low mark in a course that isn’t directly in my field of study, is something I’ve wondered.
I know GPA is not all that matters in these applications, but as I understand it, it is a big deal. In any case, I plan to take the GRE (at least in my subject).
Any advice is greatly appreciated.

According to this you can only retake courses if you receive a D+ or lower.

Somehow, I believe that that must be the guidelines for when someone must take a course, given that I know some people that have retaken courses. But, I will keep this in mind and ask an advisor. Thanks!

Every case is different, but it would probably be time better spent if you focus on doing well in the future, especially in courses in the major. A single C+ grad isn't going to derail you. Your in-major GPA will be more important than any particular grade.
Admissions committees don't expect perfection, but they do expect evidence of future success.
For your exam phobias, the university probably has an office that can help with that: a "study center" or counseling office, perhaps.

Luk'yan,
This is not an exact answer to your question, but sooner some additional food for thought. While at some departments the selection of graduate students is a very formal process run by the admissions committee, at other places things are less formal, and what matters more is the desire of one or another faculty to take you as his or her PhD student. Whether this will overweigh a low GPA -- that may vary wildly from one department to another.
Another factor to consider is whether you are aiming at a career in theoretical or experimental physics. Suppose, very hypothetically, that some faculty informs the admissions committee that (s)he wants to take you.  The committee may then look up for what courses you failed to get a high grade.  If you are to join an experimentalist group, then a low grade in a purely mathematical course will be less detrimental.  But then, again, it all depends on the style and tradition at a particular department, and on how strongly some faculty advocates your case.
In what area, approximately, are you planning to specialise in grad school?

I actually really like theory more than experiment, but both I am okay with. My current interests are in experimental AMO (atomic, molecular, and optical) physics, and condensed matter theory.


text:
The editor cannot find a referee to my paper after one year
I submitted a manuscript to a journal one year ago. The journal is well known and has already published papers on the same subject including one of my previous papers. The paper I submitted went under review after two weeks. After eight months, I contacted the journal to inquire about the status of my manuscript, I got no response. I contacted the journal again after two months, and the managing editor informed me that the handling editor is trying to secure a referee for my paper. I sent another email three months later, the managing editor said that the handling editor is still trying to secure a referee for my paper. I asked them if I could suggest some referees and they agreed.
My question is: what should I do after this long waiting period?

There is so much wrong with a journal and its community if you hear back after 10 (!) months that a paper has still not found its reviewers. What is wrong with people?

You should phonecall the editor or whoever is in charge. It's the time to make clear that behind that paper there is a  person, not just an email address.

in pure maths this is unfortunately pretty common these days

As you pointed out you have several options:

Do nothing and wait for the editor to find a referee.
Withdraw and submit elsewhere.
Send the editor a list of people who might be able to review your paper.

Nobody, including the editor, can predict what will happen if you do any of these things. Doing nothing and waiting is probably the least likely to result in a good outcome quickly, because the editor's already shown they are not able to find reviewers quickly (although there's always the chance a reviewer's time frees up and they can review). Withdrawing and submitting elsewhere would mean starting over, and there's no guarantee the editor of the new journal will be able to find reviewers either. The third option is effectively a better (for you) version of the first option, but it's still not ideal, because you can't guarantee the reviewers you suggest will agree to review either. You can only tell who might be interested in your paper.
Because there's no ideal option, you will have to make your own decision. How badly do you want to publish in this journal? If the answer is "very", do #3. Otherwise consider (but not necessarily take) #2.

I sent them a list of potential reviewers. The journal feets well with the content of the paper and it seems to me that they already received the report of at least one reviewer and for this reason perhaps they did not reject the paper, but waiting for one year without finding another reviewer is just a lot. I hesitate to withdraw the paper for the reason you mentioned ...

Anecdote that may help.
I submitted a paper to the right journal. It took more than a year to get feedback - I do not know why.
Rather than retract and resubmit elsewhere, I nagged. I emailed the editor directly, and her editorial assistant. Included the email history each time. I even telephoned once. The paper was finally accepted. I think that the editor was so frustrated and embarrassed by that point that she skimmed the paper herself, thought it looked correct and appropriate (it was) and accepted it.
This was a small low key journal, not run by a big publisher, so I could  contact the editor directly. If you can only go through the journal's web portal this route may not be available.