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Is it OK to update code on repository after publication?
Journals consider that is good practice to release script and codes to repeat the published results, and many of us I think agree with this practice. Code are typically deposited in software version control repositories (e.g., GitHub or BitBucket).
I wonder if updating the codes during reviewing process or after publications (which in my opinion is quite important, in general) remains a good practice.
Maybe the obvious answer is yes, but for example it is certainly not good to modify the data deposited for a published article (or modify its pre-print in a pre-print server).

Actually preprints regularly get modified post-publication on arXiv. You can always access the (generally inferior) published version if you want to. Of course, it is important that the authors indicate what the modifications are.

Absolutely yes!  There is no reason to stop a project from evolving just because you've published about it.
What would be good to do, however, is to identify the version current at the time of publication with a release version or other similar sort of tag. You can point to the specific tag in the publication and also have the repository tag point to the publication through its associated comment text.
This will allow a reader to have the best of both worlds: access to both the most updated information and also to the precise version associated with the publication if they need it.

Git specifically has a feature for tagging specific commits: https://git-scm.com/book/en/v2/Git-Basics-Tagging

Besides a tag or release version, it would be good to include the immutable hash of the last commit at the time of publication. That way, the reader of the publication can be certain of the corresponding code. Tags can be moved and versioned releases can be modified, but hashes cannot. They're cryptographically linked to the code.

Zenodo allows to add different DOIs to different code versions, e.g. using GitHub. https://guides.github.com/activities/citable-code/

I'd suggest adding a hash, as version numbers can be quite unreliable for some open source projects... (They do tend to work for more professionally managed software though.)

@JoL: Unfortunately, Git hashes are not cryptographically secure. But the effort required to fake a Git repository is considerable, and you would have to do it before publishing the hash, so I wouldn't be too worried about it in practice. There are far easier methods of academic misconduct.

@Kevin good tips. Whenever I output a file with some simulation results, I include the date, git branch, git revision and all the input parameters in the header. The header can get pretty long but this metadata is invaluable when you're looking at numbers that are more than 2 months old.


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Waitlisted - Got Paper Accepted - Email Committee?
I have been waitlisted to a top program in CS. During the time I applied to the program and now, I received the rebuttal results of a paper I had submitted and worked on over the last year. I got two strong accepts, and 1 weak accept, as first author at a top conference. There is potential for this paper to be an Oral paper as well.
Should I email the committee requesting to update my resume? Although having  strong accepts is usually a guarantee for admission, it is still not official until mid March, but it may be too late by then. Also, are the waitlist positions already set in stone, or can this update of my resume move me up on the waitlist. Is this even worth it to do?
Please give me your advice.

If the paper is still under review, it has not been accepted. Emailing the committee will just make you seem utterly naive.

That was my feeling as well..hmm. I have never seen anyone put "Strong accept in Rebuttal" in their resume, so I assume this holds true as well

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Rough calculation in conclusion section
In my conclusion, I imagine what my results could imply for future developments. I want to emphasize my argument with a rough calculation. Is this allowed in a conclusion section?

There are no universal rules as to what is or isn't "allowed" in a thesis or any section thereof.  You should consult with your advisor and/or committee as to whether what you have in mind is a good idea, as they are the one(s) who will ultimately decide if your thesis is acceptable.

There are no "rules". The only rule is that you should use the best arguments to explain the science behind your work, and its impact. If a rough calculation is what explains the argument best, then that's an entirely reasonable approach:

The methods we have discussed in the main part of this work have shown that with a proper formulation, optimization algorithms can lower the energy consumption of a large chemical plant by 0.5%. This may not sound like very much, but it is worth keeping in mind that such plants can have electricity costs of more than $100M per year. As a consequence, just the improvements outlined herein can lead to savings of at least half a million dollars per year. This kind of calculation shows the practical impact of the methods we have introduced herein, and clearly suggest that it is worth investigating even better formulations than the ones here.

Not best practice.  You would be better off having that in a section of the Discussion (at the end of the Discussion) with at least a paragraph of explication.  You can use an identifying subheader ("future developments", "economic implications", etc. within Discussion).
Then in the Conclusion, I would stick to more of the traditional method which is to restate the main results. At that point, you summarize all your findings.  And then give a single sentence about the implications.
I think this is better than opening a segue within the Conclusion.

Shoot.  My advice was for a paper.  I think for a thesis, things are a bit looser.  And it may not fit your structure to have a whole para on future developments within a regular chapter.

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Discussion section: Rough calculation to explain unexpected results
Unexpected results were attained in a simulation that point to a possible problem with the dataset. While writing about this in the discussion section, I'd like to elaborate on my explanation for this by presenting a simple calculation that reinforces my interpretation. Is it allowed to do this in a discussion section or should I lay the foundation for this in the method section and then include it in the results?

Generally yes. The purpose of a discussion section is to interpret your results, both in light of what was previously known (hopefully described in the introduction), and with new supporting arguments or hypotheses. A calculation (possibly short or rough) is a good way of providing a supporting argument, and it's quite common to see one in the discussion section of a scientific paper. However, theses are often subject to local rules, some of which may be silly, so make sure to check your institution's style or thesis guide, or check with your advisor whether they have any preferences.

This sounds about right. You should also consider whether you should say something in a Future Work section, as well.

I think it is fine and preferable.  This really more "analysis" than "method" at least in the context of the original study design.  Also for a reader it makes more sense in that order.
In general, there is some looseness about the exact configuration of discussion and results.  As long as you are organized and show an understandable narrative, I highly doubt you will get someone telling you "that doesn't go in that section".  I can look at papers in my field and see differences in how discussion was organized in any issue of the major journals and it is fine, no heads turned.
See also pages 8-15 of the attached:  https://ocw.mit.edu/courses/media-arts-and-sciences/mas-111-introduction-to-doing-research-in-media-arts-and-sciences-spring-2011/readings/MITMAS_111S11_read_ses5.pdf


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Description of developed algorithm as part of method or result section?
Writing my master thesis about the "Development and Assessment" of an algorithm, I'm wondering where the in-depth description of the individual modules of the algorithm and their functions belongs. Right now, the method section contains this part along with the metrics and scenarios used to evaluate its performance.
But is the developed algorithm not actually a part of the results?
Would it maybe work if I break the method section apart, as such:

Intro
Algorithm
Evaluation
Results
...

The algorithm isn't part of the results. The results are what you learned from the project - the knowledge. In this case it would be the analysis of the performance on the specified problem. The algorithm is what you built to get the results, not the results themselves.
But with the current outline, it looks like you will have to put too much into the introduction. You need to describe, somewhere, the problem and current solutions and why you want a new algorithm. That seems like a lot for the intro. Likewise you need a conclusion putting the results in context.
Note that while most of your work may have been in developing the algorithm, that isn't the essence of your knowledge contribution. The essence is in why and how this was a good approach to a problem (properly quantified) in the first place.
For example, if I build a better garbage collector for, say, Ruby, the knowledge contribution is in how and why this approach is better than other GC systems, if, indeed, it is. But you can even get a thesis out of the work if you show that the approach, which seemed promising, in fact is worse, on some scale. It is the knowledge we require, not the software/algorithm.

Thank you for your quick response! Very helpful!
Regarding your follow up about the intro: what is your opinion about the following sturcture:

Introduction
1.1 Background
1.2 Problem Description
1.3 Related Work (here I pretty much list previous strategies in single sentences and at the end, I describe all their flaws and why a new algorithm is necessary)
1.4 Objectives
Physical Parameters (split this from the intro. still packed with basic facts to understand the topic including literature)
Algorithm
Evaluation
Results&Discussion
Conclusion

I won't comment on the specifics, but, yes, something richer than the original. You might also decide to modify it as you go along.

"Method section"? It sounds like you're applying a high-level structure from natural science to a mathematics paper, which might be why it doesn't fit.
"In-depth description of the individual modules of the algorithm and their functions" also sounds off to me. Modules and their functions sounds more like the code which implements the algorithm than the algorithm per se: the appropriate place is probably an appendix, and that only because it's a master's thesis.
Pick a handful of algorithms papers from the last fifteen years and look at their structure and level of detail. You might need to use a bit more detail because you need to convince your assessors that you know what you're doing, but published papers can still give you a useful yardstick.


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Method section: small experiment for parameter setting
The size of a time-slot in a simulation has an effect on accuracy and on computational resource requirements. Trying out possible sizes (1s, 1m and 1h) I identified 1m to be the only smart choice. Defining this at an early point of the method section would greatly simplify subsequent issues like mathematical denotations and data collection. Is it allowed to do this or does all generated empirical data need to be packed into the result section?

In my thesis, I kept similar issues separately, but referred the reader to the results section discussing results and conclusions from side experiments that lead to certain decisions. This allows to use the results before they are presented in detail.
In your case, the methods could read:

Preliminary simulation to determine time slot
description
main simulation
Based on teh results of 1. (see link to results section), a time slot of 1 min was chosen.
  ...


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How to add self-study workload in the ECTS credits?
I'm applying to a Master's program in "Mechatronics", in Germany. One of the program requirements is a ECTS credits form for some specific fields.
According to the university I'm applying (Tuhh) the workload indicates the time students typically need to complete all learning activities (such as lectures, seminars, projects, practical work, self-study and examinations) required to achieve the expected learning outcomes.
I'm not sure how to convert my degree credits/hours into ECTS, given that ECTS points do include studying and assignments hours.
In my university the credits assigned in the transcript of records correspond ONLY TO LECTURES (classroom hours), where 1 credit is equivalent to 15 hours, even though all lectures are accompanied by homeworks, exams and self-study time.
I can convert the credits on my transcript but there is a clear lack of required ECTS credits. This is because only the workload of lectures are included and the self-study hours are not explicitly incorporated in the university transcript which leads me to consult how to proceed to complete the form.
I'd appreciate if someone could enlighten me. Please, let me know if more information is needed in order to calculate the ECTS.

The ECTS credits I received (in Germany) for lectures always also included the time that I should have spend working at the material outside of the lecture hall. Has this changed over time?

You can estimate it: if your previous programme expected you to work full-time on it (40 hours a week), and let's say you have 3 courses per semester, then each of these courses would be 10 ECTS (assuming equal load). As there is 60 ECTS in one year, i.e. 30 in a semester. 1 ECTS is equal to 28 hours by the way.
But calculating ECTS is hardly something you need to be doing on your own. You should approach the German university about this, chances are they have conversion tables, or at least some precedence on how to convert these figures. Moreover, the ECTS requirements is just a metric of what they actually want to measure: relevant experience. So you can also discuss your personal case with them and provide them with the study guides of the relevant courses you've followed to see if you fullfill their requirements.

According to my University in Germany (TUM) the conversion factor is 2. 1 degree credits/hour equals 2 ECTS. Anyhow, you should contact your home university as well as TUHH for their conversion formulas as your are surely not the first to have to do this.


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Does a reply to comment count as a publication?
Years ago, I published a paper with some collaborators, and recently a comment to the paper has been submitted. Together with the other authors, we published a reply to comment, which has been published on the journal.
Is it reasonable to list the reply as a publication in my CV, in addition to the original paper?

Did the comment undergo peer review?

Generally you can put whatever you like in your CV. And generally the reader will judge whether it is a real thing or padding. If the reply is truly substantive then it might be worth including it (along with links to the comment you are replying to) so that a reader gets a more complete picture of the current state of the original publication. But I would, personally, probably want to set it off as a "comment" and not as a "publication".
It is a subtle thing, though, and it requires judgement. Your judgement.

Nice answer, thank you.

I'd expand the entry, in my publication list, for the original paper by appending a reference to the reply. So the entry would look like: "List of authors, "Title of Paper", journal, volume (year), pages. See also "Title of reply", ibid., volume (year), pages."

That sounds reasonable, thank you.

My publication list is divided into sections, which in your case could look something like this (add/delete as appropriate)

Journal papers
Peer reviewed conference papers
Peer reviewed short comment
Non-peer reviewed conference abstracts

The section with the comment in it would list only one publication, but that's ok.
I generally put "peer reviewed" or "non-peer reviewed" in the section titles, because (for example) in some fields conference publications would not usually be peer reviewed whereas in others they are, so I think it helps to make it clear.
Another option is just to put a brief explanation after the reference in your publication list, e.g. "Peer-reviewed reply to comment"

Thank you for this suggestion, I never thought to list conference abstracts in my CV, so far I have only included the list of talks, seminars, lectures, etc. It might be worth using your list for grant applications.

Like you said, it is refereed. So it must be an academic publication. The ambiguity left is how much it counts for.
Well, it really depends on institutions and countries. Many top departments in top countries (like USA) will heavily discount those reply and comments; however, keep in mind that those department evaluation your contribution by reading instead of counting.
Lesser departments count more, and count comments for more.


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MSc project in ML/Computer Vision - substantial achievement
What would be a valid/substantial achievement in a Masters project (~30 pages, 4 months) in Computer Vision/Deep Learning?
Obviously it is not enough to just take an existing model (e.g. Mask R-CNN or similar), find/hack a dataset by yourself, add a layer or two out-of-the-box and finetune the model to it.
It is also obvious it can't be a huge contribution simple due to the size/nature of the project.
I'm thinking along the lines of implementing a new problem-specific loss function/accuracy metric, writing a new layer with custom functionality, and improvement of accuracy on a benchmark dataset.

This is something to discuss with your supervisor - we have no idea of what you have studied to what level and whether that topic is even relevant.

@SolarMike thanks, I'm not a student. I didn't mean this in a specific way. There should be some criteria on the degree of contribution, I believe.

But those criteria would most likely only be known to specialists in the field. You need more field specific advice than can likely be found here.

If you aren't a student, why mention MSc and tag it as Masters? You need to find an advisor, I think.

I'd disagree with your comment about using an existing model, since my MS was pretty much that -- apply an existing model to a problem it seemed well suited for, show that the results were miserable, hack it, show that didn't improve things, offer ideas for future study. Even got a conference paper out of it.

In terms of what is literally acceptable, it is whatever 1-3 people in a position of authority at any given institution will sign off on as valid. This includes projects that will go on to be published, win awards, and be seen as highly influential, and ones that I personally might see as fit for an undergraduate semester class project. Once you've moved to doing novel work grading criteria become little more than individual opinion of other academics. Move it to publication, and it becomes little more than the opinion of peer reviewers, colleagues, and yourself.

@Kathy: do you mind me asking if your project was well received?

@Alex Yes it was, and even led to a couple of professors inviting me to do a PhD with them.

What would be a valid/substantial achievement in a Masters project (~30 pages, 4 months) in Computer Vision/Deep Learning?

Whatever satisfies the people who actually certify the master's project in question.  In my department, that would be the student's advisor (and, as a formality, the department's director of graduate studies).  In other departments, that would be a committee.
Different departments and even different individual faculty, even in the same subsubfield, apply different standards for what is "valid" or "substantial", just as different publication venues (and different individual reviewers), even in the same subsubfield, apply different standards for what is "publishable".
In particular, departments necessarily set standards that are realistic for the actual population of students that they admit.  Baseline expectations at MIT may be wildly unrealistic at the University of Southern North Dakota at Hoople.
Different departments (and even different faculty) also have different philosophies about what the proper goal of a master's project should be.  Should it be a body of publishable research?  (Or more strictly, should it be a publication at a top-tier international conference like IMCL or NeurIPS, or at least a significant chunk thereof?)  Or is it sufficient to produce a useful piece of software, say for an industry client, or a well-written expository survey?  Or is it sufficient to attempt publishable research and settle for a useful implementation or survey?

Obviously it is not enough to just take an existing model (e.g. Mask R-CNN or similar), find/hack a dataset by yourself, add a layer or two out-of-the-box and finetune the model to it.

No, that is not obvious.  In some departments, that would be considered a valid Master's project.  In my opinion, it wouldn't be a very good Master's project, but my opinion only matters for students in my department.

thanks for the input. Could you elaborate what constitutes a good MS project in your opinion?


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Main results vs ablation study in a journal paper (deep learning)
I ran a number of experiments (object classification/segmentation), and got some good results vs a range of benchmark models. The paper progressed to major revision, and most criticism concerned the lack of ablation studied.
Essentially, what the reviewers want to see is the same experiments on the same data, but with a variation in the model's architecture (make it simpler, roughly speaking), in order to establish, that the more advanced architecture is in fact useful.
So, what happened, is that in some accuracy metrics simpler variations of the main model in fact outperformed it.
So here's my question: how can I incorporate this fact? One obvious solution is to point out that the main model still outperforms other in some metrics, but I have a feeling it's not enough.
What else can I say?
PS: this refers to the results, discussion and conclusion sections.

Do you have any justification why your initially chosen parameters should constitute the "main model" instead of the better ones found in the ablation study?

@GoodDeeds well, not really, I just came up with this arch. and it worked well. Technically I can replace the 'main' model with a simpler one, and then present the more involved ones in the ablation study, but first I'd like to know if I can use the current setup


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Submitting a paper to a peer-reviewd journal after putting it on medRxiv
Most COVID-19 related papers(about 2/3) go as pre-prints on arXiv/medRxiv, and so I decided to do the same. Is it still possible to submit the same preprint to a peer-reviewed journal? In such case, are there some rules for bypassing the double-blind review? After submitting, I got an automatic reply from JMIR suggesting a submission to one of their journals. So it seems to be possible, at least.

I don't think many journals do double blind review these days do they? Certainly every paper I've ever reviewed has had the authors names on it.

Most journals allow this, probably pretty much all of them. If you look at a journal's Guidelines for Authors, they should normally state that this is fine (occasionally it is probably elsewhere but this information should be given on the journal's website). For example, "Statistics in Medicine"'s guidelines say "Statistics in Medicine will consider for review articles previously available as preprints. Authors may also post the submitted version of a manuscript to a preprint server at any time. Authors are requested to update any pre-publication versions with a link to the final published article."
I'm not aware of specific rules for peer review though - I do realise that "double blind" doesn't really mean "double blind" in this case, but what can they do? (Some journals got rid of double blind peer review because authors could be identified in too many cases too easily anyway, this being one of the reasons.)

"probably pretty much all of them" depends a lot on the field. Medical sciences is lagging a bit, and although there has been a lot of movement into accepting submissions that exist as preprints (even just in the past couple of years), some journals still don't allow it.

Do you know/can you recommend a journal of reasonable high standing with rapid reviews of Coronavirus AI submissions?


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Research reference or source for study before selecting thesis topic
I would like to do my master thesis on image processing. What will be best approach for study and selecting topic on this field?

A Google Scholar search, maybe? http://scholar.google.com/scholar?hl=en&q=image+processing

Can you please clarify what you are asking?  Right now, this question is terribly broad...

As currently stated, this seems like a generic question on how to select an MS thesis topic, so I have closed it as a duplicate of another question asking exactly that. If the duplicate does not address your question, please [edit] your post to clarify what you are asking and it may be reopened.

A master's thesis assumes that you will have broad general knowledge of a subject, and detailed knowledge of a particular area of the subject.  Whether you are expected to include an experimental component or make a contribution to the body of knowledge beyond that which results from organizing material into a thesis depends on your institution.  Your advisor can help you there.  (Image processing seems like it could lend itself to any number of interesting experiments, but I speak as one who knows little about the field.)
So, you start with a relatively recent overview book and absorb that.  Consulting with your thesis advisor, pick an area of concentration.  Find a few recent papers in your area of concentration and absorb those.  Then read the papers those authors cite, and read the papers which cited the papers in your initial reading.  Using the citations, you will be "working outward from the middle" until you have a thorough grasp on your area of concentration.  Particularly, looking at papers cited by recent authors should guide you to the fundamental work in your area of concentration if you haven't found it already.
While you are becoming an expert in your area of concentration, also look for gaps in the knowledge of that area.  One of these gaps will become your thesis topic.  Work closely with your advisor so that you don't pick something that your faculty will consider trivial.  Beware also of the "solve world hunger" problem; you probably have two semesters to complete the thesis.  You cannot solve world hunger in that time.  You want to be somewhere between "order lunch" and "solve world hunger," but more in the direction of "order lunch."

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How formal should a recommendation be in the US?
I am a lecturer in a European university. A student from my department asked me to write a recommendation for a program somewhere in the US that he wants to attend.
I have read the horror stories about American recommendation letters, where apparently "He is not only quick at learning and good at solving complicated problems, but also with a logical and creative mind that enables him to raise some insightful views. I was also deeply impressed with his diligence and outstanding communication ability, compared with my other students." is considered lukewarm(!) and grounds for rejecting the applicant.
I have found a few sample recommendation letters and advice from different universities/people around the internet and I've used them as inspiration to spruce up what I had initially written. I have also asked colleagues, but understandably they mostly write letter for other European universities, where such superlative language would usually be reserved for sarcasm or toadying.
However, one thing that is rarely consistent is how formal the letter should be.  More precisely:

How should I start the letter? "Dear colleagues"? "To whom it may concern"? "Esteemed organizers"? Similarly, how to end it? "(Best) regards"? "Sincerely yours"?
How to refer to the applicant in the letter? "Jane"? "Jane Doe"? "Mrs. Doe"?

I would rather not penalize the student because I do not understand foreign cultural norms.

I wrote several references for students who got into jobs / further study in the US and never have I resorted to such flowery language (using 17 words when one will do) in any of the references. Sticking to statements about punctuality, attitude and performance - all the reference letters fitted on one side of A4. But, of course, there is the possibility that they got in inspite of my reference...

I certainly sympathize with your situation as I've recently written some letters for a former work colleague for semi-academic type jobs, and I have found it difficult trying to avoid certain unintended interpretations while maintaining honesty about someone who I think is an excellent candidate. Nonetheless, I think the main issues with the italicized quote you provided is its non-specificity. Much better than the first sentence would be something like the following: (continued)

"An example of his insightful views and creative approaches is his submitted paper An analysis of ... co-authored with X, which arose when, in a seminar presentation by X a year ago, he asked whether Technique T developed in a series of recent papers by Y could be suitably modified to answer a certain question raised by X in the seminar." Of course, the biggest problem is finding something like this to say.

A good recommendation letter needs to first establish that the recommender has had extensive interactiont with the student.  Most of the European recommendation letters that I've read don't succeed in this, either because the author hasn't actually spent much time working with the student or because the author doesn't think it important to include this in the letter.  Students from smaller liberal arts colleges in the advantage have lots of opportunities to interact with faculty in this way and get better recommendation letters as a result.

Just be sure to cover how you know them and their performance and accomplishments when working with you. You can have the student write a summary of this much for you even. Then the rest can be typical flowery praise or whatever. I barely look at them (except to check for anything negative) unless someone in on the borderline.

Formality is the wrong parameter to worry about.  Write at whatever level of formality you are most comfortable writing to your target audience.  (But err on the side of formality, unless you know your reader personally.)
The parameter you should worry about is credibility.  Your readers don't just want to know that you think highly of the student; we want to know why you think highly of the student, and why we should trust your judgement.

He is not only quick at learning and good at solving complicated problems, but also with a logical and creative mind that enables him to raise some insightful views. I was also deeply impressed with his diligence and outstanding communication ability, compared with my other students

This is not a terrible recommendation letter because the praise is insufficiently strong; it's a terrible recommendation letter because the praise is vague.  Which complicated problems?  How do you know he has a logical and creative mind?   What insightful views?  How did he show diligence?  How and where did he demonstrate his outstanding communication ability?  (And do you mean speaking, writing, or both?)  And why should we trust your judgement at all?  Be specific.
Without these details, this letter looks like flowery boilerplate that could be applied to anyone.  The letter says nothing specific about the student, which makes me think the writer knows nothing specific about the student.  Moreover, the letter says nothing about the writer's expertise, strongly suggesting that he expects to be trusted merely because he's old and tenured.
In short: Show, don't tell.
The "horror stories" page you link to gives similar advice.  (Did you actually read it?)

I would suggest that unless you have other information, such as a relationship with the recipient, that you write more formally than informally.
But if you want to write the sort of purple prose in your example, you should also back it up with facts and examples. "...has great insight. For example, ...". If it is all just superlative generalities it might be too easy to dismiss, though I wouldn't think it was sarcasm in a letter of recommendation.
If you know the recipient, or have a reputation that implies that they know you and your work, then less formality might be fine. Some people will simply be believed based on their reputation.
But, lean toward facts and formality, I think. And note that if you praise someone who shouldn't be praised it will come back to haunt you and your institution.
Note: This is personal opinion about how I would react.


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Citing a reference multiple times
I am trying to write an introduction to a grant proposal (not for actual research, but because it is part of an assignment that was given to me as an organic chemistry student). I am trying to reference a paper multiple times, and I was wondering whether or not I am supposed to use the same superscript number that corresponds to the reference I am citing every time I cite the reference in my paper. Do I use the same superscript (or different superscripts) every time I cite the reference, or do I only need to include a citation once?

If you are using a numbered referencing format (rather than an Author,Year format), there should be one numbered entry in your reference list for each individual source you reference.
Use the same superscript throughout the manuscript to refer to that reference; it might appear once or it might appear several times.
The exception to this rule would be if you are in a field that uses footnotes. Footnotes are a different matter entirely.
Ideally, you should get used to using a citation manager even at this early stage, it will make your life much easier now and in the future. Your citation manager will handle a lot of this sort of thing for you once you've learned how to use it.


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Getting credit/ownership for improved software
I recently made some changes to a piece of (proprietary) code that my group uses which has made it two orders of magnitude faster.  The code I updated wasn't mine and the original algorithm IP was published a few decades ago so I can't claim I did anything other than some clever refactoring/parallelizing (which somehow everyone else said wasn't possible).  The impact of this update is such that work that would have taken months can now, in principle, be done in under a week (or from hours to minutes).
Unfortunately academia doesn't really reward 'enablers' for improving software so I'm not really sure what I can gain from this beyond some ideas in my own PhD that were not possible previously.
The critical point, compared to other questions I've seen on this topic, is that the code is now commercially viable.  Understandably my supervisor is very happy and wants to keep things under wraps for the time being.
I'm aware that the university probably owns every line of code I just wrote. Do I have any ground to request compensation if the software starts being licensed?  I don't want to sour the relationship I have with my supervisor which has up until now been very good (and I've just earned a lot of respect for this work).
If I was working in industry this is about the time I'd be going to my line manager and at asking for a salary bump or a promotion.  In academia it seems like this sort of work is relegated to a pat on the back and a footnote.  I suspect I'm being sour, but is this just the way it goes?
Am I allowed to ask that people cite the software even if it's not a publication (not that we have a website!)?  For instance one can cite R, Numpy, etc.

"I'm aware that the university probably owns every line of code I just wrote": The university will have an IP policy that will explain explicitly whether this is true.  You should probably read it.

The copyright vests in the university for software.  It gets tricky because the original code was funded through a grant pot several years ago and as mentioned - the stuff I haven't re-written is clearly not mine. I'm building (however significant the changes are) on old code.  Either way, I don't think I have much ownership rights to it.  Not so fussed about that, I'm more concerned about recognition for the work.

"Unfortunately academia doesn't really reward 'enablers' for improving software" [Citation required]. I could pull a bunch of papers that are just reimplementations of previously published software. Not to speak of the new capabilities it enables (you could publish a paper dealing with a problem that would had taken years).

Earning "a lot of respect" has certainly some non-trivial value. And it is possible for sure that it indirectly leads to monetary value too.

As a software developer it is hard to believe that improving a piece of (proprietary) code can made it two orders of magnitude faster. Although parallelization can make it 2-5 times faster on a modern workstation of 6-8 cores, unless the original code was notoriously bad it is hard to imagine that it can really be faster by two orders of magnitude (~100 times faster) just by improvement, without changing the original algorithm. So, are you 100% sure that the acceleration you get is legit? Sometimes (especially with parallelization) when things are too good to be true, there is some subtle condition which usually breaks by parallelization. So, first make 100% sure (compare results produced for a wide range of input data) by the two versions of the software (the old and your version). I assume you use some version of version control system (who does not?), so you still have the old version somewhere. It does not matter if this experiment takes a few days - 1-2 weeks it has to be done to be 100% sure that something did not break and you do get identical results between the two versions of the software for a wide range of input data and not just by a small test case.
If you are 100% sure that you really improved the software without breaking anything, the main question is did you actually improved the original algorithm or not. Simply adding an OpenMP directive and parallelizing a code which was parallelizable all along, is not a publishable result. In this case, your improvements do not merit a publication and therefore no publication => no citation, since you did not create the  original software. On the other hand, if you did more than refactoring / parallelizing the software and your contribution is significant you must publish these results on a technical-focused CS conference. Then everyone using your version of the software could cite this work and additionally could cite the online version of the software if it is publicly available.
On the legal version of your story, I really do not have the expertise to answer. In this case, I would search the IP policy of the university as @NateEldredge suggests and ask an experienced lawyer who knows about software patents. I do not think anyone of us here are really entitled here to give legal advice. Of course if your version of the software starts getting money for the university, you are probably entitled to a share and you must protect your rights as good as you can. It is just that right now, we do not know if this software is going to actually become a product for sale.
Also about your paragraph:

If I was working in industry this is about the time I'd be going to my
  line manager and at asking for a salary bump or a promotion. In
  academia it seems like this sort of work is relegated to a pat on the
  back and a footnote. I suspect I'm being sour, but is this just the
  way it goes?

I do not know how much experience you have in the software industry, but be rest assured that you do not get a raise everytime you do a good job. After all, this is expected from you and it is a prerequisite for you keeping your job for a long time. You can always ask for a raise, but that does not mean you will get one.
On the other hand as I mentioned earlier, either you changed the software's algorithm and implementation so much that you deserve a separate publication or you bug-fixed a crappy code (which you will use on your PHD) which does not really say that much. Either case, this is probably the only credit you will get.

Yes.  I improved single threaded performance by around 20x (overall), changed a few sections which were incredibly inefficient and then got linear speedup by threading it.  It was a classic case of poor academic code, and yes, I version controlled it and checked repeatedly against the original to make sure the results were still valid.  And yes, the speedup is 'legit'.
Sure, I wouldn't go asking for a raise now, but when my performance review came up I would certainly mention that I saved the company potentially thousands of hours...

To expand a little.  Everything is versioned with git.  Each revision is checked against the original on a variety of different test cases.  The runtime is directly proportional to the input size and I have plenty of results using the original software to check.
But thanks for clearing it up, I figured it probably wouldn't be citable but I think it would be foolish not to check.

I suspect my best bet would be to attempt to make a novel modification to the code that wasn't testable before (due to the amount of time needed to test/iterate) and publish that.

Adapting software for GPU can definitely get several orders of magnitude while not being completely obvious.

The most simple solution is to publish these new results. The question to this answer can be found here:
In which journals should I publish my software?.
This is the most appropriate thing to do. Some journals also have something like the ``OUP Bioinformatics Application Notes''. Check, together with your advisor, if you can find something like this.
The possibility of monetary compensation of some form is probably low. Not only because you are in academia, also because you most likely work as some form of public servant. Details are different for all countries and work places, however.

I mentioned compensation because I also work in industry. We've had several projects where we've had to offer clients alternative software because the code I refactored was too slow to be practical (even though the results are normally superior).  I doubt it'll come to that, but as I mentioned in another comment - I'd rather find out my options and get nothing than never ask and never know.

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


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scholarships/fellowships/funding not available to Masters in the US and UK
Is this generally true? If so, how to find those scarce sources of them?

please clarify your question. an intro explaining the problem would be good.

In the UK, from what I've seen, yes. If you don't have enough cash for a UK masters, I'd say don't bother and go somewhere else.

@ Alexey do you think a uk masters is very expensive? mayb an american one is more expensive

Depending on what program you are looking into, the universities (at least in the US) should have grants and fellowships predominantly based on merit. (Some grants may be issued by the university based on proven financial need, but it is often not much and there does need to be a need). Your best option is to see what fellowships are offered by the university and apply early on, as most deadlines for the fall are early January.

Thanks. Do you have any rough estimate of how competitive of each scholarship scales like? 1/3, 1/10, 1/100?

I cannot say, as it usually depends on the program and university. I would talk to the financial aid office and maybe ask more from an advisor of the program.

if i didnt get funding before being admitted, is there money available after starting school? anything other than RAs and TAs?


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TOEFL IELTS GRE scores expired but with work experiences in English speaking countries
If one wants to apply for grad school in the USA, and one's TOEFL, IELTS, GRE scores all expired, but one has all the following experiences able to prove ones' English proficiency:
one did an exchange student program in an English speaking country;
one has work experiences in English speaking countries;
one has published many papers in English.
Will these be sufficient reasons to persuade the admission office and pass their English requirements?

Only the individual programs can answer this question for you as far as the flexibility of their policies.

Go and get new scores - "hopefully" they will be better than the original ones...

If a school requires test scores and they’re expired, you will likely be required to take the test again. Some schools may accept expired scores for evaluation purposes but will require valid scores to complete the matriculation process. In many US public schools, the TOEFL/IELTS scores are required to establish ability to work as an RA or TA, so having valid scores is necessary.

@ aeismail will the applicant b rejected for not having up to date english scores?


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apply for a Master's, already holding a PhD in a similar field
If one has a PhD in a similar field and goes apply for a Master's, will that hurt his/her chance of getting accepted? In the Statement of objectives, one can argue for some slight nuances between the PhD obtained and the desired Master's. Other reasons could be that the Master's school is a top school or wanting to move to the area the Master's is located in.

I think the expectation is that if you already hold a phd, then you already know how to research the "similar field" on your own and do not need the second masters.

@ Buffy not really. this posts emphasizes on 'similar field'

If I were looking at that CV I would wonder why you had bothered, and worry that you just wanted to be a student for longer.

MS programs can be money-makers for the university, and already having a PhD in any other field would not likely be a problem for you in getting accepted to a program. On the other hand, were you hoping to apply to a similar PhD program, that would be prohibited by many top schools.

@ Rafael_Espericueta so for top schools, do they also need to make money from MSs, then accepting a phd holder?

For example, UC Berkeley has an MS program in Data Science. Having a PhD would not be a problem; that shows you have the ability to complete their program, so should improve your odds of being accepted. But you'll need lots of $$$!

@ Rafael_Espericueta Yes, lots of $. Is it hard for current masters to apply for funding in the middle?

Often such MS programs offer no funding for their students. But many students enrolled in such programs are working full-time, and their employer often will pay at least some of the fees.


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To do another Master's, already holding a PhD
If a STEM PhD holder applies for a Master's in another STEM major, would this be an advantage or disadvantage in the eye of the admission committee?

Is there a reason you are considering a masters over a postdoc?

Reposting my comment because I didn't realize it had gotten cut off: Can you be more specific? Applying to an MEd or a speech path master's (or other professional degree) might get different answers than applying for a biology master's when you hold a psych PhD.

A friend recently did this. It's going to make it very easy to get in.

need more specifics: Which country you are in? What are specifics of PhD and Masters degrees? What is desirable outcome after getting master? AFAIK, masters are mostly paid degrees (you pay), so more available than PhDs

@ noslenkwah it's another major than my phd, so i'm not eligible for doing a postdoc in a new field

@ Azor Ahai i have a phd in physics and might consider doing a CS master's

@ Marcin i'll b interested in hearing more about ur friend. what's his/her background

@ aaaaa i have a phd in physics and might consider doing a CS master's. i wanna do it in the US. i dont wanna pay, so will look for scholarships

If you ever want to leave academia, it could be seen as a disadvantage. It suggests you are a "perpetual student" rather than someone who actually wants to do some (real-world) work.
The main point of a PhD is not that you learned some (random) snippet of new information while doing it, but that you demonstrated you can learn new stuff on your own with minimal supervision.
That is what you should expect to be doing for the rest of your working life, either inside or outside academia, but expecting to keep getting more "awards" for doing that is rather like a kid in school expecting to get another gold star for every good piece of homework they turn in - most people grow out of it.

Very opinion based and narrow minded answer. See the other answer for a bigger horizon

In view of the above comments, let me try to give a slightly more constructive (or at least more detailed) critique of this answer:
This does not really answer the main question on what the admission committee would think, but sort of challenges the premise of the question whether doing a Master's after a Phd is a good idea in the first place. Considering the value of that decision seems out of place here: the answer to it is highly dependent on the motivations for obtaining a Master's and therefore needs more context than is given here, or at least a much broader perspective.

@ alephzero of course a phd can learn anything on their own. but most of the time employers prefer candidates holding a related degree than being able to self learn, dont they.

@ Discrete lizard i need to jump into another field where there're more jobs. academia is too crowded

Surely you're joking Mr. Feynman!
Sorry, but you walked into that joke. Actually, such an application would occur so infrequently that it might result in a few chuckles. But I don't think it would have a lot of effect. But certainly not a big advantage.
In fact, people, including myself, will wonder why a person would bother. After all, the applicant can study and learn effectively and evidenced by the doctorate, so what is the need of a formal program. It might be a disadvantage in some places where the available slots are limited and people would feel they should be given to someone who needs the training more.
On the other hand, if a lab needs particular skills that you have, they might be interested, just for that.
Thus, it is impossible to say in general as local needs/beliefs will dominate such a situation.

I have seen a number of people with multiple Masters on their CV. - The advantage can be getting additional knowledge in a related subject quickly. A Masters takes 1 (UK) to 2 (rest of Europe) years, while a PhD takes at least 3 (UK, 4 years limit) to potentially 6+ years. - In addition, it can be easier for people to do a part time Masters than a part time PhD to extend their knowledge. It also avoids the repetition of the introduction from an undergraduate degree.

@DetlevCM Perhaps the most prominent example I recall is Michael Griffin, the former head of NASA.

@DetlevCM You're comparing a master vs a PhD or undergrad while Buffy is asking why someone who has shown the ability to learn information on their own would need any formal program at all to pick up new information. You can find the books, papers and exercises without troubles online so giving a limited spot to someone who doesn't really need it, instead of someone who has yet to learn all those essential skills might be considered bad use of resources by some (and yes, there are certainly some immaterial advantages to studying in a formal program that you won't get from self-study, I agree)

Major cases: to be a licensed engineer you must have a degree in engineering. So if you get all your degrees in a non-engineering field and then decide you need engineering licensure, you have to take a Master's. This also applies to some science fields like geology, you need a degree in the field.

@user71659 Licensing or similar bureaucratic requirements would be the key reason I can think of. My wife suspended her PhD program at ABD status to get a master's in education because she decided to teach high school. She tentatively plans to resume her PhD after she has her full license, but the Masters became an urgent and separate requirement once she made the decision.

The advantage of a formal program is that it gives you the required money and time to study the material. Changing field is hard enough; doing it while working full time in order to pay rent is extremely difficult.

@ Buffy of course a phd can learn anything on their own. but most of the time employers prefer candidates holding a related degree than being able to self learn, dont they

@ user71659 holding 7 degrees, a perpetual student. did the degrees help him?

I would guess that most employers aren't "collectors of credentials." They want competence, of course, but no matter how obtained. You want to be able to produce things, not just study them.

Not a direct answer to your question, but a personal experience. I got a PhD in EE and am now one semester away from finishing my masters in CS. Three years after my PhD, I changed careers from EE research to a data science. My EE PhD provided me background in linear algebra, partial differential equations and numerical computations. The primary motivation for me going into MSCS was to develop intuition in certain areas which I wasn't exposed to, but became important in my new career: combinatorics, statistics, probabilistic modeling, optimization, operating/distributed systems, and computer networks to name a few. Following a masters curriculum guided me on what areas are (roughly) considered important and also brought a (forced) discipline to my studies.
If an application of MS followed by a PhD crossed my desk, I'd laud your discipline, but also probe on why you went that route. You need to have a good answer for that.

@ RDK very good answer. seemingly ur EE phd and CS MS look quite similar. then u had an argument to support the necessity of doing the CS MS

In terms of competency, I can't imagine why it would be seen as a disadvantage. If anything - it shows that you are capable of successfully completing an academic program.
The only scenario I could imagine where this may be an issue is if the Master's program is affiliated with some scholarship program, where the scholarship terms & conditions require that the applicant does not hold an advanced degree. If you're applying for a non-scholarship program then I can't imagine why they would reject your application - you are willing to pay good money and are likely to successfully graduate.
Another issue might be if you're applying to a STEM program that's very far from your PhD degree (say, from theoretical physics to zoology). If your bachelor's degree does not fit the prerequisites for the program you may have an issue, and the PhD won't help (but probably won't hurt).
Good luck!

"Huh so the guy finished their PhD and then instead of working in their chosen field and applying their knowledge they decided to instead enroll in a different field, mhmm I wonder why". That's the first thought that would go through my mind if I saw that CV on the stack of job applications. So there's certainly some possible downside to it.

At the very least it would make me want to interview this person and ask them why, not outright reject them.

I'm with Voo. I can think of reasons to get a master's after a PhD, my wife is doing something analogous (suspended her PhD program at ABD status), but it calls for a real reason such as licensing requirements or moving to a radically different field with almost no overlap.

"it shows that you are capable of successfully completing an academic program." Didn't the undergrad degree, the PhD and possibly the master's from before the PhD already prove that two or three times? Why go back to prove it again?

@ Voo i need to jump into another field where there're more jobs. academia is too crowded

@ Spark great. but r u part of a university committee of that sort?

I did sit in my department's admissions committee for a while, why do you ask?

@ CJ59 i did a good phd but not good enough for a good and easy career in my current field

@ Spark then ur opinion is very important to me. so a MS is easier to get accepted than a phd, because a MS applicant initially will just pay. is it hard to acquire funding in the middle of the MS?

Would not be any purpose of doing two different STEM MSc:s. After one you are supposed to be able to learn similar level stuff even faster on your own.
I could understand wanting to do an economy MSc to complement your STEM knowledge. Quite some people ending up as CEO or CTO of medium or large size firms seem to have double degrees: one in tech and one in econ.

It's a plus on the side of competency to complete it, but a concern on the side of whether you would actually enroll and finish the degree if you are accepted.  But the school, year and discipline of the PhD, the school and discipline of the Master's, and why you are switching play hugely into it.  Also, frankly, your standardized test scores and ability to fund your own education, just like anybody else.  I'd recommend talking to an admissions person at the school you are considering, as well as a hiring manager in the field you are considering.  (BTW, I'm a PhD in Management Information Systems who was in academia for several years but have spent the last 12 years in industry.)

@ Larry Seligman my english test scores all expired but i dont want to retake them again. if i argue i worked in english speaking countries for quite a few years, would that be convincing?

For me personally, it would not be convincing since doctoral programs are so reading and writing intensive.  But that's just me.  I'd recommend contacting the admissions department of the school you are interested in, as well as the department chair of the department of your interest.  You should do that anyway; putting a face to a name is always a big plus, and for doctoral programs the department has most or all of the decision input.  You can also give the department chair first hand experience on how well you can interact in English.

It really depends on the field of previous research but this is becoming more common due to more and more academics going into interdisciplinary research. It's not uncommon for folks from Biology to want to go into mathematical biology or even data science which requires more maths/computing. Therefore, if your previous PhD was in a different subject area to the masters you're applying to, that should be fine. Your research skills will definitely be valuable and may even help you get into a postdoc after completion of your masters. I've seen so many examples of academics with non-stats PhDs in the UK going back to study masters in statistics for example.


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whether necessary to continue to work on unfinished academic work
When one finishes a degree or a research position, the boss asks to carry on sth unfinished (unpaid), does one need to agree to do so?

no yes-or-no answer. just wanna hear ppl's opinions

No, you don't need to agree to do it at that point, unless you already have agreed or committed previously. However, for your future career it would be good to give it some consideration, at least, and to work in in if possible.
I'm assuming that "the boss" is a professor, actually, who can aid you in the future.
But "unpaid" is a big issue. If you can get something back for your efforts either hard currency or academic currency it would be a good thing also.

Context would seem to be important here. If there are papers to finish writing, then yes they should do so - the work done should be documented. Now, barring having a next position, yes, the professor should probably keep supporting the student.

@guest2, I don't think obligation is the issue unless you previously agreed. Strategic thinking is called for. What is best for your career as you see it.

@guest2 - Perhaps we envision different scenarios. If a PhD student graduates and goes to a post-doc, but refuses to finish up the last few papers (and there are always papers left to do), that is not good. If the post-doc leaves to take a permanent position, and refuses to finish up the last few papers, that is not good. It is not good for either the student or the advisors. Now, if a student finishes up, has no place to go lined up, and the advisor wants the work done but won't support them, well, there is an issue at that point.

I think Jon Custer is envisioning academic work as a collaboration between students/postdocs/whomever and the PI, rather than work done for the PI. Therefore, the end of the funded arrangement is not necessarily the end of the commitment to the project. I agree with this perspective. For the good of all academia, it's normal for people to continue projects when they've moved on to a new position; everyone gains and loses from this.

@BryanKrause - and I would add that, if somebody does abandon the work unfinished, they really can't complain if somebody finishes it up for them and submits it (with appropriate authorship).

No. And profs typically "lose" some work because of this.  It is just a function of the system.  I wouldn't cry about it either as you have your life to attend to.
I definitely would not stay at school doing this versus going to a job.  Or forego some "break" vacation type activities before your real job starts.
I would draw the line at doing any new experiments. But writing something up is different.  It can benefit you also.  But you now have a little more control in the situation.  Don't be obvious about it, but do it on "your terms".
If you are still in academia, figure out a way that it benefits you (e.g. continued collaboration).  But concentrate on "WIIFM".  You don't have to be prickly. But just only do things in away that benefit you.  Not guilt trip over unfinished work.  (The universe will always have unfinished work and it's not like the prof is in the lab on Xmas , head down over the bench, to make sure 100% work is finished and 0% grant money wasted.  Of course science wants a high return on investment, but some waste is normal.  And you need to look out for you, not the PI, not the agency.  (If they REALLY cared, they would pay!)


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apply for faculty while working in industry
For a department focused more on industrial interactions, will going to work in industry for a while before applying for a faculty position in that department be recommended/helpful?

It depends on the field.  It is much more likely to work if you are teaching in a professional program, as opposed to a liberal arts program.

what do u mean by professional program

Nursing, Law, MBA, ....

in my case not like these, tho the department stresses on industrial interactions

I would think that you should consider a somewhat different question. What is the best path for me, now, to obtain a faculty position later? You probably have several options and each of them takes some time to implement. Which is the best path if the goal is to become a productive faculty member?
The two main pathways would, perhaps, be more education and some time in industry. Either can probably be good, but I would suggest that further/deeper education is probably going to be more valued than industry experience, with one exception.
If you were to find a unique, cutting-edge, industry position that puts you in contact with top-level research and development in an area that is seen as vital at the time, then that would be a nice thing to brag about on your CV. But working as a drudge in some mid-level outfit won't really help you advance in academia. These top-level positions are pretty rare, and may not be open to you with your current background.
Note that the top-level industry experience I'm mentioning is the sort of thing that you can bring back to the university to build a research program an/or give important advantages to students.
I think it is easier to find a way to stand out in the educational realm if that is where you want to be eventually, than it is to go and then transition back with the same level of excellence. But that is more opinion than fact, of course.

If you describe the field a little more, people can advise better. Perhaps there are still generalizations (helpful to others), but also you will get some tailored answers.
But I will say in general that even in rather applied subjects (chemistry, geology, engineering, etc.) that it is the norm not to have much industry experience.  Even in topics like business.  Doesn't mean it will hurt you per se.  Or that there is nothing leverage-able.  But the Academy seems to value the Academy (not saying they are right or wrong to do so).


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whether to make a tenure track faculty job talk interactive
Is it appropriate to give a tenure track faculty job talk in an interactive way, like posing some questions, asking for audience opinions?

What would the point be?

I expect that different members of the audience would have different reactions to interactivity in a job talk. My own reaction would be negative.

Engineering background here. Wouldn’t recommend this!

the point is to show an interactive way of teaching in the future

@feynman But I don't think the goal of job talks is to demonstrate your pedagogical technique/skill - to my understanding, the goal is to demonstrate your research achievements and potential. Granted, I'm on the younger side of things (= postdoc) so I don't really know what I'm talking about, but everything I've heard makes it hard for me to imagine a situation where this would be a good idea, at least in my field (mathematics).

In the right circumstances you can. For example, if you are studying color vision and have worked on the dress it might make sense to poll what color people see as a way to highlight the ambiguity. I job talk I saw on the psychology of magic, involved magic tricks and breaking them down. It was useful. If you are going to interact, it really needs to be critical to the talk.

for scientific context, would posing questions to the audience look nicer than just giving a monologue


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addition of physical address upon paper acceptance
A paper was reviewed, sent back for revision and resubmitted. Is it allowed to add a new address (current) when a paper is just accepted?

This may be country or field dependent, but, assuming the work on the paper was mostly done at the old address, one would indicate a current address as a footnote (style varies by journal). Adding such in proof is usually OK.

will a footnote be useful in promotion to tenure?

That is a very different question that can only be answered by the particular institution. But if your tenure decision comes down to one paper, which by date of acceptance might not count (or show the work performed at that institution), you are probably on thin ice already. Properly attribute work. Otherwise your graduating students might just switch their affiliations at the last moment, taking credit towards tenure away from you.

Probably.  But only the journal can say and you should just ask them ASAP.  Worst that can happen is "no".
Edit:  removed non-SE compliant sarcastic remarks.


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recommendation letters at different stages of interviews
Recommendation letters today become less and less important in affecting employers' final decision, though they are often requested at different stages or even before any interview. What to do to avoid requesting letters too often, annoying letter writers?

Why do you believe that recommendation letters are less and less important? For academic positions, they are critically important! You might want to revise the text of your question to be more specific: "Will asking your references to provide letters of reference many different times annoy them?"

did u have experiences where ur letters helped u land a job

Other than the obvious choice of not asking for reference letters until a reasonably short list of candidates has been selected?

@BrianBorchers almost. or how to explain to employers that u wanna defer requests of letters

@feynman -- let the employer choose whatever approach to letters they think is appropriate. You can't change it anyway.

@feynman: I will also note that a good approach to pretty much any kind of formal writing -- including on this site -- is to use proper and grammatically correct English. Using "u" instead of "you", "ur" instead of "your", "wanna", etc, is not a great way to ask questions in serious forums. Nor is a great way to get a job -- something I know you're interested in.

@feynman Yes. Not only my own current job, but dozens of faculty that I've helped hire as a member and chair of my department's faculty recruiting committee.

@JeffE but a mutual fit might be more decisive than letters?

Not a chance.  No (or bad) letters, no interview.  The letters are literally how we tell whether someone looks like a good fit.

What to do to avoid requesting letters too often, annoying letter writers?

You don't request letters “too often”.  You request letters once, at the beginning of your job hunt: “Would you be willing to write a strong recommendation letter to support my applications for [kind of job]?  I'm planning to send out about [number] applications.”  If they say yes, take them at their word.
At least in North America, academic/research employers request letters directly from your references, not from applicants.  Applicants only provides names and contact information for their references; they never see the actual letters.  Most universities send letter requests by email; a few ask references to submit their letters when the applicant submits their other materials, without waiting to be being asked directly.
Keep your references up to date on which [kind of job]s you've actually applied for, and how they should expect to receive the letter request.  I strongly recommend maintaining a single Google spreadsheet (or your favorite equivalent) with a row for each target institution, and columns for each of your references to indicate who has asked them for letters, and which letters they've actually sent.  (Then your references can see which of your other references have already submitted letters, making it less likely that they'll fall behind.  Peer pressure works.)

that's right. some do ask applicants to send letters or have their writers send, rather than the employers requesting the writers directly. for applicants with a very long job search cycle like 1~2 years, requesting letters over a long time can annoy writers can't it

If you're worried about your references getting annoyed, be sure to reveal up front that your search will take 1-2 years (giving them an excuse to decline), and ask how to minimize their annoyance.  Then take them at their word.  (The only time writing more letters annoys me is when great people don't get jobs and have to keep applying.  But then I'm annoyed at the employers, not at the applicant.)


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junior professor's strategy of postdoc recruitment
If the professor has 15 publications and a postdoc applicant has 10 papers, will the professor think the applicant is too strong to colloborate well as to not obey the professor's ideas all the time?

Being a young professor I will not hesitate to hire an applicant with a profile even stronger than mine; especially, if I feel that postdoctoral candidate has good plans which will be beneficial for my research group. My own Postdoctoral experience was very good, my professor never treated me as student, rather a peer colleague.  Also, in my opinion a professor who want an obedient postdoc is not a professor I would ever consider to work with. In academics healthy criticism is the best feedback on your work and the way to improve.

This is the correct way that a professor should handle the situation. However, I think that there definitely could be professors that act in the way that the OP is worried about


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Writing sample for Economics PhD: empirical or literature review
I am applying for an Economics PhD and I need to submit a writing sample of 2,000 words. I am planning to take an extract from an article I published, but I am unsure about whether I should take the literature review or the empirical results + conclusion.
The upside of the literature review is that the language has more coherence. The empirical results section consists mostly of descriptive sentences, graphs and tables. On the other hand, I can imagine it would be good to demonstrate my capacity for statistical analysis and reasoning. Any advice on this? I'd really appreciate it.

Honestly, I would pull either the intro or conclusion. It would give a sense of the overall paper in terms of question, method applied, and results. Personally I would lean towards the intro.

When I look at an applicant's writing sample, I want to see that they can write professionally and convey research in a compelling and clear manner. I expect coursework and letters of recommendation to speak to a candidate's capacity for statistical analysis, I am looking to the writing sample to understand your capacity for communication.
To this end, my preference would be to see 1) Intro 2) Conclusion 3) Theory/methods section. Perhaps you could get both intro and conclusion in 2000 words?
Of course it would be preferable to submit the whole paper, so I would recommend sending a PDF with a link to the full paper embedded and including the full paper citation at the beginning.

@David Helpful answers are typically upvoted Or accepted (using the check mark). Welcome!

Since this is published research, I would certainly expect to see the whole paper submitted with your application in any case. It follows that using part of the paper also as a "writing sample" is useless.
I would contact the committee and ask whether, since you have published research, it can stand in for the "writing sample" they ask for. If they nevertheless want both the whole paper and a "writing sample", or if you don't get an answer on time, you should prepare a "writing sample", which should then be in the spirit of a "Introduction and motivation" of a research paper, down to describing the subsequent sections of this yet-to-be-written paper.  This section will show command of language and of concepts, ability to defend the value of a research topic, and also how comprehensively you plan to explore the topic.


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To what extent do doctoral advisors "pick" their grad students?
I am just starting a graduate program in physics. I have read a few posts describing what a PhD student should think about when looking for an advisor, but I have a question regarding the advisor's perspective: what do graduate advisors look for, generally speaking, in their prospective advisees? I.e. what is the relative importance of research background, grades, and other factors?
I have been told by some older students that (assuming there was sufficient funding) if there is a personality mesh and the student's work ethic is solid then an advisor will tend to accept a grad student, or is the process more nuanced/competitive?

In some countries the school you graduate from is everything. In France it is almost impossible to get a decent* advisor in mathematics if you didn't graduate from an ENS (Lyon or Ulm), or from Polytechnique. *By decent, I mean whose influence is strong enough to support you for tenure. Soft factors like personality isn't usually evaluated (how would you do that reliably?) and don't matter (at least, not until the PhD phase has started)

I feel like I've read a similar question before, but can't find it.

A very small number of academics receive very many applications.  Most get relatively few applications and have few choices.

What country are you asking about? In many countries, supervisors are decided before starting a PhD.


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Possibility of doing Masters in astronomy with only bachelors in CS
I have a bachelors degree in Computer Science & Engineering and currently employed in s/w industry in Pakistan, but have no degree in physics. For long, I've been interested in doing research in physics, especially in astronomy, astrophysics or in particle physics.

Are there good institutes or universities in Europe ( Germany,
Sweden etc) which accept students without any degree in physics to
Masters program in astronomy or astrophysics or joint with computer
science? If so, do they also offer financial assistance or some form
of scholarship to such students to meet at least one's tuition fee
expenses?
Where I can find some research article that some teachers are working on so I can contribute them? I want to help through my coding skills. How to found those teachers who are working on research based on astronomy and contact them?

I don't know about Europe, but in the U.S. the lack of a degree in physics would not by itself prevent your acceptance, but instead the concern would be with documenting that your ability and knowledge of physics is sufficient to favorably compare with those who are admitted to the program.

Why do you think you're interested in doing research in those areas? Only from some curiosity or have you done some related work at some point? Why do you want a master's degree? Are there universities local to you that might hire you to assist in research, leveraging your programming skills?

I don't think so. Physics bachelor degrees in Europe are very intense. I have not seen any subject where you go so fast so deep through different mathematical concepts as in a Physics bachelor's, not even math studies themselves (although physics courses often skip proofs or long derivations; or introduce them later). They might admit you if you prove you somehow have acquired the skills of a Bachlelor's grad, though.

I can't speak for all the institutions, but in general, you're out of luck. It's true a lot of modern astronomy is programming, but there's also a lot that isn't. You need to be familiar with things like the Fourier transform, vector calculus, and classical mechanics / general relativity.
Here's an example of the entry requirements for astronomy at Lund University in Sweden.

Bachelor’s degree of at least 180 credits in physics or the equivalent. The degree must include at least 90 credits in physics. Proficiency in English equivalent to English 6/B from Swedish upper-secondary school.

You'll have to get the physics training if you want to pursue this, unfortunately.


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Is it possible to register to a conference after the deadline
I was accepted as a participant for this conference but unfortunately, I completely forgot to register and pay the fee.
The deadline was May 30, and the conference starts on Jul 25.
What should I write in an email to apologize and ask if it's possible a late registration?
(I'm not a speaker, but I'd have presented a poster)

By "accepted as participant", do you mean that your poster was accepted? Or something else?

No, I mean just my participation (I haven't made the request for the poster yet)

This looks unusual to me. How did you get accepted? Usually, at least in my field, the way one applies for participation is by registering and paying the fee. There is no separate, parallel system for accepting participants.

For acceptance, we send a motivation letter explaining our background and expertise and then, if accepted, we proceed with registration (this step basically is just the payment of the conference fee).

Keep the apology short and to the point. Keep the request short and to the point.

It worked, they have registered me


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IEEE full article with small images or more than 8 pages
I'm writing a full article (6-8 pages) using IEEE guidelines.
Currently got two versions: one where images are more readable, and another where 4 images to be read need a lot of zoom.
In the first case, the article has 10 pages in total (3 columns are references). In the second case, 8 pages in total (3 columns are references).
I know from fact that

References most definitely count (for the page total). IEEE page limits are inclusive of
  any front and/or back matter. And it is a HARD limit—not even a single
  word should spill over onto an additional page.

I don't want to have the images like that where the reader needs to put on extra zoom but i also want to respect the total page limit.
Is there a way the images can be placed after references (or anywhere in a specific section) that makes them not count for the total page count?
If not, considering the images are very relevant and both the content and references were reduced as much as i could, what can I do in this situation?

Does this answer your question? Splitting a relatively long paper into two shorter papers

And this may be relevant: https://academia.stackexchange.com/q/103361/72855

It's for a conference that requires to follow IEEE guidelines. It's good now!

If the article is only going to be published online, one can create hyperlinks to access the full sized images.
If it is to be printed, one can reference or add notes saying that a full size version of the images are available in the website X.

In many, but not all IEEE publications, the hard limit implies that if the paper is larger than N pages, every (N+1)th page is charged with an overlength charge. See this page on IEEE Author Center, which also contains the fresh link to a PDF with current prices (overlength, open-access, color).
Usually, IEEE Transactions on XXX will allow publishing papers that are larger than standard size (up to a certain maximum), while the IEEE XXX Letters-type journals might have a hard limit with no possibility to publish a paper exceeding the standard length even for an extra fee.
I would certainly check the journal (not the general IEEE guideline) you are intending to submit on that matter since you want the images to be legible without a mandatory zoom. The fees vary, but, for example, IEEE Transactions on Antennas and Propagation (TAP) charges $200 per extra page (as of 2020). See this 2018 guideline for IEEE TAP which covers more details on how references count and fees are calculated.

Make it into two - part 1 and part 2, gives you more pages in total as well. There are often papers published that have “subsequent” papers. An example: part 1 is method with some preliminary results, part 2 further results, analysis & conclusions.


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Molds of PhD thesis from more than one idea
I'm considering doing a PhD in  Software Engineering and Information Technology.
Associated with a particular concept of interest (immersion), got many ideas running through my mind that having them explored would bring, at my sight, both business and educational value. So, the ideas:

Consolidation work.
Understand the current state of the art in immersive technologies.
Create taxonomies.
Design and implement immersive solutions.
Investigate the real-world value of immersion.
Etc.

Spoke with two PhDs. One told me a valid thesis can be a collection of articles that have to be published; in other words, what I have in mind is definitely good and possible as long as the articles are published. The other PhD told me  this would be something too general and I need to specify more to have a valid and good thesis; in other words, grab one idea and specify even further.
So, what I would like to understand is if I could create a thesis taking what I've got in mind with the 5+ ideas and have it be considered a valid and good thesis? If yes, under which molds / structure / methodology?

Let me suggest that you are trying to decide things too early. It is good to have a lot of ideas, but you need a thesis advisor to help you refine your ideas to be successful. Many would object to so scattered a list of things. A doctorate requires both breadth and depth, but the dissertation is focused on depth, which requires specialization. But I don't know the actual academic culture of Portugal, so can't say definitively.

This is country and doctoral school specific. Contact first your advisor

@BasileStarynkevitch ok that's where I should start first then - defining the specific school. The PhD doesn't necessarily need to be taken in Portugal, got some opportunities in UK, USA,... being considered. Spoke with my advisor and managed to get some very interesting feedback (will share as an answer ASAP).

Don't rule out Australia as a destination ;-)

As long as you have a good list of publications by the time you graduate, I don't think a defense committee is going to stand in your way because the research wasn't "connected" enough. Especially considering that the different aspects you want to explore are definitely related.
But you're putting the cart before the horse I think. You're very unlikely to be able to make a complete exploration of such a broad area as you've described above. So don't think of that as "your PhD project," think of it as "this area is my research interest." Your PhD work may only delve into and develop a very narrow sliver of that research interest, and then your later academic or corporate work would be related to other aspects.
Also, research questions tend to look a LOT different when they're finished compared to when they started. You start on one line of inquiry and get side-tracked, or pushed off course by various difficulties, or you just find something exciting opening up along a parallel track. As a PhD researcher is more or less your job to be open to those course-corrections. It's very rare to enter into a PhD with a certain research question in mind and exit the PhD with the sense of "Yup. Nailed it." More likely you accomplished only 10-20% of what you set out to do, or maybe even 0% because you switched to something totally different. That's good! The free-wheeling path of discovery (on a good day) is the essence of academic research and separates it from more goal-oriented corporate work, where answering THAT question your boss needs answered is more important than following your nose and personal interest.
So, I think both answers you received aren't as different as you think, they're sort of two sides of the same coin. Yes, your PhD research doesn't need to be part I, II, and III of the same research question. It could be multiple loosely related works. However, they will still probably have a reasonably consistent thread between them, and be more exact than the very general notions you've bullet-pointed above, simply because your research direction and research interests will gain clarity and focus through the PhD process.

A bit of caution is advised. A bunch of unconnected papers may represent a "significant body of work" or not. So, "good" in the first sentence is very important.

This varies a lot from field to field, so take this with a grain of salt. Before I started my PhD, I envisioned doing lots and lots of stuff. Unfortunately (or fortunately actually), that isn't how academia works. Developing a (good) project takes time. Also, more often than not, easy and good ideas have already been explored which means that, if you want to work on a particular topic, you have to build on top of what other people have already done. For instance, during my PhD, I developed 4 different projects over a period of 4 years. And that is considered above average in my field. Talk to your supervisor once you have one (or if you already have one). They are there to guide and will provide with the answers that you need.

Your question is a sensible one. Here are a couple of points which may help:

Every thesis is about something. It must be coherent and focussed on responding to a single problem or question (this can be broad or narrow, but it must be coherent);
It must make an original contribution to research. Typically the best way to show this is to show what others have done and why their attempts at answering the question specified in (1) above are insufficient (normally done in the introductory chapter(s), but can be re-stated throughout the thesis);
A GOOD thesis is both readable and useful. You need to be able to tell the story of your research, and engage your reader in the process and demonstrate some potential for impact. If you can't communicate what you're doing your research will have less impact.

The points above may seem obvious, but they are fundamentally what a PhD is about.
Your question about thesis by publication actually pertains to two different aspects of completing a research degree (i.e. research masters or PhD):

Structure; and
Assessment (examination).
A thesis by publication entails a topic structure where sections of the thesis appear as (often edited) stand-alone articles. These are normally 'topped and tailed' with an introduction and conclusion which demonstrate a coherent response to a problem or question (1 above) and highlight both originality and potential for impact (2 above). They will hopefully also help to make the thing readable (3 above).

BUT
Formally committing to submit your thesis 'by publication' in most cases also commits you to having those publications accepted for publication in journals of an acceptable standard before you can complete the degree. This therefore forms part of the assessment (or examination) of your degree.
While having a 'by publication' topic structure can be a good fit for some projects and lead to more publications during candidature (which we like) - it can sometimes commit research degree candidates to more constraints when it comes to examination than they really need.
My advice would be to consider this carefully before committing to a PhD 'by publication'. Sometimes you can achieve the same thing by simply negotiating with your advisory panel a topic structure which will allow you to develop your thesis chapters in a form very like publications - which you can then go off and publish - without committing you to having those published in exactly the same form as appears in the thesis.
This may sound like a minor point but can lead to major frustration in cases where candidates are basically ready to graduate and have completed their thesis but are having to mess around with journal submissions when they could be out there publishing anyway with a degree already under their belt.
Something to think about, anyway.
Some resources are included below (most will come up in Google Scholar with a link to the full text), and good luck with the project!

Phillips, E., & Pugh, D. (2010). How To Get a PhD: A handbook for students and their supervisors (5th ed.). London, UK: McGraw-Hill Education;
Dunleavy, P. (2003). Authoring a PhD: How to plan, draft, write and finish a doctoral thesis or dissertation. New York, NY: Palgrave Macmillan;

[Note - there are a million books on how to write a PhD of the 'PhDs for dummies' variety. Most of these are crap. The two books above are the best. Timeless classics :-)]

Chinneck, J. W. (1999). How to Organize your Thesis. from http://www.sce.carleton.ca/faculty/chinneck/thesis.html;
Brien, D. L. (2008). Publish or perish?: Investigating the doctorate by publication in writing. Paper presented at the The creativity and uncertainty papers: The refereed proceedings of the 13th conference of the Australian Association of Writing Programs;
Davies, R. E., & Rolfe, G. (2009). PhD by publication: A prospective as well as retrospective award? Some subversive thoughts. Nurse Education Today, 29 (6), 590-594. Available at http://www.sciencedirect.com/science/article/pii/S0260691709000185;
Durling, D. (2013). Understanding the PhD by publication. Paper presented at the 2nd International Conference for Design Education Researchers, Oslo, Norway;
Niven, P., & Grant, C. (2012). PhDs by publications: an ‘easy way out’? Teaching in Higher Education, 17 (1), 105-111;
Jackson, D. (2013). Completing a PhD by publication: a review of Australian policy and implications for practice. Higher Education Research & Development, 32 (3), 355-368;

To get a PhD, you will have to specialize. This takes time and effort so if you want to make a contribution that is valued in your field and serves your future career, you will probably have to select one topic and run with it.
That said, some of the best research comes from merging ideas from different topics. Look at Nathan Myhrold. He is an extremely successful researcher but he engages in fields from astronomy to paleobiology to Nuclear reactors. Working on one topic allows him to get ideas for another one.
What I am trying to say is that as a PhD student you will have to specialize to be effective, but don't give up the other topics that you are interested in. They might serve you to keep your academic career running after your PhD. They might even give you ideas for solving problems during your PhD.
As for starting your PhD, do not worry too much about which one of the five topics to work on. I am guessing this will solve by itself within the first year if not sooner. First of all, your professor will probably have an opinion. And once you start to dig deeper, you will have a better idea about it yourself. The PhD research topic does not need to be defined from day one. You will have some time to understand what is it that feels most interesting and promises most for your future career.


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Is it appropriate to contact a journal editor when they have already decided to accept a paper you refereed?
I had an unusual circumstance happen to me this week.  I had earlier refereed a paper for a top journal.  For the first draft, I recommended a fair number of changes, but I felt that if they were all made, publication would be appropriate.  There was also another referee, who opined that the subject matter of the article was not important enough for the journal.
The authors revised the manuscript and resubmitted it.  The associate editor sent it back to the same two referees.  The other referee basically did not budge, still saying that it was not worth publishing.  I, on the other hand, recommended moving forward with publication, provided the authors made one more change.  It was something that I had mentioned in my first report as well, and it represents a genuine error that really needs to be fixed.
At this point, faced with conflicting reviews (and possibly after a request from the authors), the associated editor sent the paper out to a third reviewer.  Just the other day, I got a communication from the editor that he had decided to accept the paper.  Included were the current manuscript version, the authors' responses to my second report, and the positive report from the third referee.
What struck me was that the authors had not fixed the mistake that I had pointed out in my first two reports.  The response in their resubmission letter to it seemed to have completely missed the point.  I was puzzled about what to do at this point.  Eventually, I decided to shoot off a letter to the associate editor, reminding him that the authors had not actually addressed my one remaining objection.
I'm still not sure whether this was an appropriate thing to do.  I apologized in advance and said it might be none of my business in the letter.  I do have a pretty good relationship with this associate editor; he sends me a lot of papers and had nominated me for a refereeing award.  I guess that, apart from what opinions I hear here, I will find out what he think of my writing to him.

Yes, it's appropriate, and the worst thing that can happen is that your advice will be of ignored. You are clearly trying to do your job as referee as conscientiously as possible even when that means going the extra mile. I can see why you got recommended for a refereeing award.

@DanRomik Sounds like an answer.

@zibadawatimmy thanks, I was afraid someone would say that... It's kind of a borderline case, but I decided it's more of a comment than an answer so I'd prefer to keep it that way.

I always wondered how some papers, that obviously still contain easy to find errors, could have made it through peer review. Thanks for showing me that it doesn't always have to be the reviewers fault.

Out of curiosity: does the journal charge authors for publication?

@CapeCode It was one of the Physical Review journals, which do not normally charge for publication.

As I have now heard back from the associate editor, I can give an answer to my own question.
The editor was quite appreciative of my note.  Here is what he wrote back to me:

Thank you for your note. I am sorry that we did not realize that the authors have not satisfactorily answered to the criticism in your second report. If you can send us quickly a note that we can forward to the authors, we will have them take it into account before proceeding with publication.

I quickly put together a detailed explanation of what was still wrong with the manuscript and sent it back to the editor.  I'm not sure precisely how things will proceed from here, but I am gratified that I apparently did the right thing.

Good to know that there are editors doing editorial work.


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Professor asked for details of letters I need
I am applying for summer REUs in physics. A professor I asked agreed to write me a recommendation, but also asked for details of the letters I need. What details should I send?

Please have a look at this: http://ksuweb.kennesaw.edu/faculty/rbrow211/recommendations/index.html

The professor wants you to help him/her write the letter. You know what the institution needs and the prof doesn't want to have to explore it separately. You have an opportunity to let him/her know just what you would like emphasized in the letter.
Some professors even ask for a first draft of their letter and may send it out pretty much unchanged. Make sure you include enough to cover the needs of the granting institution and enough to highlight your own work, especially as it is known to this professor.