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Why do most American universities offer funded PhD positions but not similar opportunities for Master's programs?
I've noticed that in the U.S., universities commonly provide funding for PhD students in AI/ML fields, including scholarships, assistantships, and fee waivers.
In contrast, Master's students have fewer funded opportunities and often rely on loans or work-study programs.
Can someone explain the reasons behind this difference in funding structures?

What fields are you looking at? This is field specific. Most research-based natural resources (e.g., wildlife, forestry, fisheries) have fully funded MS positions. Conversely, humanities often do not have fully funded PhD positions. Also, can you improve your question by including examples?

Just replace the phrase "funded positions" with "researcher employee positions" and your question will almost answer itself.

https://academia.stackexchange.com/questions/202251/why-do-american-universities-typically-have-scholarships-for-bachelors-but-not-f

Here are a few reasons:

Long-term Benefits and Market Demand: Universities expect greater long-term benefits, a.k.a. money, from Ph.D. research, as the research output often attracts more funding, creating a self-sustaining cycle for funding Ph.D. students. Conversely, Master's programs are primarily self-funded through tuition fees. This is feasible due to the typically high demand for these programs, ensuring their financial self-sustainability.
Research: Ph.D. students are primarily researchers, contributing to the university's academic output, a role less common with Master's students.
Teaching and Funding: Ph.D. students often serve as teaching assistants, a cheap teaching solution for universities, compared to hiring faculty members, and a key reason for their funding.
Commitment: Ph.D. programs are longer, and require greater commitment. Funding helps ensure their completion and, additionally, attracts top global talent, which is essential for maintaining a university's research reputation.
ROI of Master's Programs: Master's programs are professionally oriented, and designed to provide specific skills for the job market. Graduates are expected to secure higher-paying jobs, justifying the tuition investment. These programs often lead to immediate employment opportunities, offering a quicker return on investment, and are closely aligned with industry needs, providing a direct pathway to advanced professional roles.

Big $$$ thing on your first bullet - professors get grants to do research, and pay students out of them. PhD students are worth the money (around for years to learn and get things done). Masters students don't have the same payback at all.

The difference is even more clear in Europe. As a master student you are a student - anything that the university "gets" out of you is a happy, but ultimately unexpected, side-benefit. As a doctoral student you are staff, and it's commonly expected that staff gets paid.

@xLeitix That also depends on the european country and the funding. As a PhD student you are still often more a student (although not taking classes but doing research). Or a sort of staff or something in between if the funding gets you a real contract in sufficient amount (rarely 100%, but at least one has also the scholarship and some student benefits).

@xLeitix you want to mention that the master diploma is a somewhat hard prerequisite in most of Europe. We hire (or fund) fully educated professionals for their research towards a doctorate.

@VladimirFГероямслава Absolutely true that it depends on the country (and the field), but all fields have juniors, a PhD 'student' is just a junior employee. Just because you're learning and somewhat inexperienced doesn't make you a student. Maybe 'apprentice' would be a better term than 'student'.

@DavidMulder You literally and legally have the student status as a PhD student. Including the student benefits (taxes, ISIC,...). And receive a student scholarship and are enrolled in a study program. Also, some do not even get the work contract when they start although it is better now than how it used to be a decade ago. In some countries all PhD students are employed by the uni, but not everywhere.

One reason, not yet mentioned, is that large, state supported, universities in the US, have a mission to support the common good. An educated public is essential to that end, providing broadly educated citizens that can drive toward a better future, both economic and otherwise. But that is balanced by limited resources and pushback from taxpayers whose individual wishes don't always mesh well with the needs of the general public.
So, a bachelor's degree is seen as a start, well worth supporting, with further education funded otherwise. Even doctoral students are supported mostly with teaching assistantships, not scholarships, so that those students actually contribute to the undergraduate program in exchange for their funding. Most large bachelor's programs couldn't operate without the support of those TAs. When I was a doctoral student the overall math department had twice as many TAs as faculty members. The TAs were all doctoral students. So, the two, support for undergrad and support for doctoral "fit" together nicely. Without support the doctoral students wouldn't be there and without them the undergrad program couldn't function.
Masters programs are sort of caught in the middle. The students may not have time or experience to be TAs and the funds available are pushed to the lower levels with, hopefully, more impact, hoping that masters students are willing to self-fund for a couple of years in the hopes of higher salaries. This is probably short sighted, but competing interests are at play.
Also, note a subtle distinction. The states, and their universities don't "fund" doctoral students. They fund research and some of that funding flows to doctoral students who participate in it, often in essential ways. And they provide low wage teaching assistantships and (usually) free tuition to doctoral students, but those students have duties to perform in return for that funding. Again, the computation is that this system maximizes the return on expended funds and supports the common good. You can, of course, question the validity of that computation.
Sadly, we seem to be moving to a world with less support for education overall, not just higher education. My own education was richly funded, though I completed degrees in the early 1970's. Things started to go the wrong way (IMO) about then, when we landed on the moon, "winning" a wager against the Soviet Union. It was, I think, the "fallacy of the last move" that suggested that we won, once and for all, and that support for a highly educated public wasn't that important a goal anymore. I've noticed steady decline since. My grandson will have no such luck. It saddens me that universities are dropping such programs as history and philosophy in favor of (only) STEM, and my path was math. A narrow, technical, education isn't adequate to support our future in my view; either for the individual or for society as a whole.

The reason is the economics of masters and PhD programs. Both generate revenue for the university but in different ways.
Masters programs make revenue by charging masters students for an intensive 1-2 year sequence of courses. In return, the students get improved career prospects via their new knowledge and having "Masters in Data Science from Big Name University" on their resume. The university profits from the tuition dollars, hence why masters students get charged.
PhD programs don't directly generate revenue, but they provide skilled labor on the cheap via research and teaching.

research: academic departments charge a percentage off the top of all research grants awarded to professors in their departments. But to get grants in the first place, professors need to do the research. PhD students provide the cheap research labor.
teaching: professors are very expensive. To reduce costs, universities pay PhDs a very modest stipend to do teaching, and especially to handle more menial work like answering questions and grading

I know that sounds cynical... but it's also true! When you strip away the flowery prose about the pursuit of knowledge, and just follow the money, this is what you find.

Why Do Most American Universities Offer Funded PhD Positions but Not Similar Opportunities for Master's Programs?
As a broad statement, I would say this question is false.
This question is specific to programs.
Some humanities and social science programs offer unfunded or partially funded PhDs.
In contrast, many natural resource programs offer funded MS programs.
To expand upon the other answer, look and see if programs are "professional" or "research" programs.
Some observations I have seen comparing the two types of programs:

Professional master's degrees are sometimes Masters of Art degrees (MAs), Masters of Engineering (MEng), or similar titles, and research programs are Masters of Science degrees (MSs).
Professional programs often have more coursework and only a limited capstone project or thesis whereas as a research-based program will include a thesis that commonly produces journal articles.
Professional programs tend to be tuition-based. Students are the revenue source. Research programs often occur in fields where MS projects get funded by grants (like the natural resource fields). Students do the work that completes the funding requirements.

Also, sometime service department with heavy teaching loads will use masters students to teach and provide TAs.
Depending upon the size of the graduate program, these TAs may be open to professional masters students.

Unlike other countries where it is typical and even necessary to obtain a masters degree before a PhD, that is not typically the case in the US. Undergraduates can apply directly for a PhD and begin after they've earned their undergraduate degree.

Academic institutions serve two somewhat separate purposes in the US as in many places: first, they serve to educate students. Second, they perform research to push forward the knowledge of all humanity. In the US, education of students past the high school level is a cost mostly (and increasingly so) paid for by the students themselves rather than the government, whereas government continues to support research.

These two features sets up a bit of a two-track system:
Masters degrees are an add-on to a bachelors degree (which ordinarily students pay for) that help the student make more money in an industry career. Students are expected to treat the degree as an investment in their future and pay off the cost through their future earnings.
PhD degrees are the apprenticeship start to an academic research career and serve the broader mission of furthering academic knowledge. PhD students often work as employees on research projects, as teaching assistants, and in other ways that support their education while they are earning the degree; direct scholarships (often called "fellowships") are relatively rare. While doing this work, they are paid far less than what a similarly educated professional would earn, so even if they do not pay tuition they are still paying a substantial opportunity cost at least for their earnings in the short term, and possibly for their lifetime.
Generally, it's more difficult to apply and be accepted to a PhD program, so if a university has jobs available that could fund either a PhD or a masters student, it's natural to fund the PhD student because they will be there longer, funding them today helps the university's academic research mission in the future, and because in some sense they're "better" than the masters student: bluntly, if the masters student was more qualified and interested in the university's research mission they should have applied for and been accepted to the PhD program.
In my view, the biggest problem with this system is what to do with people who are trying to collect more credentials to apply to PhD programs, especially people who were unable to do research as an undergraduate (even more so those who were unable to do so because of financial disadvantages that affected the type of institution they attended or their available hours to do student research versus work another job to support themselves or their family). A masters program might be a good stepping stone, but someone who completes a masters and then starts a PhD will be in debt for a long time (perhaps indefinitely) before their earnings have increased sufficiently to pay off the degree.

Why should someone pay for your short term excursion in academia? In MS you actually can’t accomplish anything. The goal of the universities is to run their research machine and for that they need PhD students.

"You can't actually accomplish anything" seems like a ill-founded statement that lacks an empirical basis. Moreover, (i) it is not the goal of all universities to run a research machine, and (ii) it is most definitely not the case that only PhD students can contribute meaningfully to good research.

authors: Vladimir F Героям слава


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How do some PhD students get 10+ papers? Is that what I need for landing good faculty position?
I've been looking up some PhD students' websites, and there are people who somehow got 10~30+ total papers with 5~10+ first author papers. Many such students are in computer science, but there are a few in fields like bioinformatics. Some garnered 100+ citations before graduation.
How did they do this? This makes me uneasy about my chances for a tenure track position in the future. I just finished my 3rd PhD year at a decent US institution. My field is closely related to bioinformatics, and I am aiming for a tenure track position in a similar field. But if my top competitors are of such caliber (10+ papers 100+ citations), I'm guessing my chances are slim.

Figure out what job you want to get.  2.  Examine the record of people who have that job.  3.  Do better than they did.  This is different from what you have been doing.  Many PhD students never apply for tenure track jobs, and many of the applicants have not been PhD students for some time (this varies by field).

I can guarantee you, that a high number of papers and/or citation still doesn't guarantee a faculty position (personal experience).

@BasJansen The relevant question here is not if good metrics guarantee a faculty position, but if someone with less-than-stellar metrics still has a chance to get a faculty position.

@lighthousekeeper I was just challenging his underlying assumption that to get a faculty position he needs to have good metrics, which isn't true and therefore neither is the reverse.

@BasJansen OK, that was not clear from your comment.

It is not necessary but it is not a bad idea to starts publishing while working on your Ph.D..  The best thing to do is talk to your faculty, in particular your dissertation advisor.  He/she knows your ability, knows your field and can recommend subjects that YOU can write papers on.  You might start by co-writing one or more papers with your advisor.

Bear in mind that the number of papers somebody "normally" finishes a phd with is VERY field-dependant, and probably also somewhat country-dependant. In some areas, zero is common.

@Anonymous Physicist - yes but how do you do step 3? Aye, there's the rub.

Obligatory SMBC reference: https://www.smbc-comics.com/comic/2011-03-29

I think at least part of the answer lies in different cultures across fields. I did my PhD in computer science/artificial intelligence. There a huge focus is on conference papers which tend to be smaller contributions. Often incremental progress on a single project is reported in multiple conference papers and it was expected that a paper corresponds to several months worth of work. Frequently you would publish in a conference and then have an extended version appear in a journal. All in all, 5 first-author papers upon PhD was not exceptional. Also we had a lot of within-group collaboration so I got to e.g. run a few statistical routines on someone else's data, help write the manuscript and become a coauthor for about a week of work. I ended my PhD with 23 publications, 8 of which were first-author - this was above average in my group, but not exceptional.
Now I do bioinformatics and collaborate a lot with biologists. Their papers are usually longer and for any result you need a lot of tedious manual work in the lab. In turn, the papers represent years worth of work. Many people - even brilliant ones - end their PhD with 1-3 first-author publications. I've heard in some areas, publications are even harder to come by. In other words, the number of publications is not a very good proxy for brilliance, especially when you are ignoring quality and comparing across fields.
As for the 100+ citations - my best bet (since you mention bioinformatics) is that this is because the students co-authored some software/tool/protocol that ended up being useful => cited. (tool papers tend to be the most cited ones). This is obviously a success, but once again does not necessarily imply that failing to produce useful tools is a sign of non-brilliance.
Example: DeSeq2 software for comparing gene expression across samples has > 10 000 citations on Google scholar while the first detection of gravitational waves has just above 6 000 citations on Google Scholar.
Also me and some of my colleagus have landed reasonable jobs with roughly 0 citations (excluding self).

My son has just completed a PhD in Electronics Engineering in the UK.  He has one paper from his PhD (which was first author), and a second from his MRes course before he started the PhD.  He has got a position as a Research Assistant to continue working on his PhD topic.

The gravitational wave paper is from 2016, the DeSeq2 paper is from 2014.  In both cases this is about 2k citations/year.

@ZeroTheHero maybe it is not the best example, although I guess it is obvious that a (well done and useful) simple software is a very different league than a breakthrough in physics. But also note that counting only citations since 2018, DeSeq has 6740 while gravitational waves have 2810, so if anything, the DeSeq paper is accelerating :-)

First, that's not a useful question to ask, primarily because it's nothing you can control in any reasonable way.
Second, just because some graduate students have somehow come up with such statistics does not imply that your average competitor has. It's a bit similar to the average physicist not having published three papers at the age of 27 all of which could have gotten a Nobel Prize on their own -- even though Einstein did. You will always have people who are far better than everyone else, and they will likely get positions somewhere, but they're not going to fill all available positions.
Finally, publications are just one measure search committees use to determine who to hire. There are many questions on this forum that discuss the many many other criteria used, so I won't repeat them, but you might want to read through these other posts to see that publications are really just one of many criteria.

"First, that's not a useful question to ask, primarily because it's nothing you can control in any reasonable way" At least one can surely control the probability of attracting more citations, specifically, by focusing on a "hot" PhD topic. That is not to say that such approach is definitely the most desirable.

It is still a useful question to ask even if you can not do anything about it.  High school basketball stars should consider that their chances at an NBA career are basically zero and plan for a future outside the NBA.  PhD students should make a realistic assessment of their chances of an academic career and plan accordingly.

All fair comments, though of course I meant to imply that you can't control others writing this many papers.

Then it's still a useful question to ask: possibly one can use the answers to improve one's own productivity and impact.

Well, I guess that too is a fair comment :-)

As someone who got 6 publications during their PhD - it's often because they are of low quality. I (wrongly) placed a large focus on quantity over quality and it resulted in a rather lacklustre thesis.
Some people are able to get large numbers of high-quality publications, but they are so much more rare than people who get large numbers of papers that will never be cited or even read by anyone of note.
It's good to have some publications - but it's better to ensure that the research you are doing is of value to the field!

It's good to have some publications - but it's better to ensure that the research you are doing is of value to the field - quotable quote!

better this romanticized approach than publishing garbage

There are some institutions where there is common practice to put ones peers as co-authors even if they had nothing to do with it. On top of this, there are these "paper-producing factories" where the main objective is just to produce paper after paper.
I'm not saying that these individual geniuses with these citations honestly doesn't exist, but personally I'd be cautious about just accepting them right away as the truth and instead consider a bulk of them to be untruthful.

Relevant link: https://academia.stackexchange.com/q/134006/111810

How did they do this?

One possible explanation is that people sometimes stumble over a vein of gold. You make a small breakthrough with a new idea that you can then expand in different directions, apply it to and combine it with other phenomena, often in collaboration with experts for those phenomena.
The obvious follow-up question is to find such a vein of gold. Luck might be an important component here, but a good intuition might play a role as well -- sometimes, the intuition of the involved advisor and collaborators. For the collaboration aspect, an advisor with a strong network, as well as good networking skills of the PhD student can help.

Citations are not always the best of indicators. In my post-doc position I was co-author on a paper that had a "whacky new" idea. We didn't really develop it too much. We just said "hey, you can use this thing here to solve that problem over there, isn't that interesting?"
So this has resulted in a lot of people saying "yes, and if you tidy it (Reference [1]) this way and add this feature, you can get an interesting variation on it like so." Where [1] is the paper I was co-author on. Some thousands of papers have done some such thing. And I was alphabetically the first author. Though I was quite clearly the least contributor.
So I technically have an excellent citations stat. But I left academe after my post-doc, and barely remember doing this work. So I'm absolutely not good material for being a prof. Both my co-authors have distinguished careers. But they were both established before this paper.

This is highly dependent on your research topic, publishing culture, and local standards. I will try to answer from personal experience.
As a PhD student I have published 15 papers. Roughly the same amount of manuscripts came from work developed during PhD, while others derived of work done as an undergrad and Master student. All of which were published in reputed peer-reviewed journals, though mostly low-tier journals.
This is how I achieved this: (i) passionate about research; (ii) passionate about writing and editing papers; (iii) some equally passionate co-authors; (iv) working like crazy; (v) being stubborn like a mule; (vi) prioritising descriptive reports within a small research niche; (vii) getting completed work published.
I had finished my PhD with roughly 60 citations. I don't think I have a good citation record nowadays, but I have published many papers.
Did that help me in my career? Sure it did. Academia is hungry for publication counts almost everywhere, and prospective postdoc supervisors assume you'll earn them at least that. Most PIs are scared of unfinished projects, and depression-stuck collaborators.
However, how such numbers are seen varies between different academic cultures. Therefore I cannot say whether I'd specifically recommend this path to anyone. You wouldn't believe the stress (and politics) involved in pushing things forwards, especially if you work with rather laid-back mates.
The key point to keep in mind is: how can you show value? Focus on that.

There are some topics which are inherently good for publications and citations. If you need a specific dataset for your study, this is quite often very difficult to build up. So if one does the work, a lot of people will use and cite your dataset. Even more so, if there are only limited ways to gather such a dataset, especially if you need patients with a specific disease or something like that. In these cases the academia is happy for any dataset they can have, and therefore it gets easily published.
If you look at the published papers, there will certainly be some paper on "here we made this dataset, feel free to use it and cite us", then after this comes the "we now evaluated this dataset with our methodology" sometimes followed by "with this methodolody we made this workflow and product" and so on. Sometimes accompanied with some more datasets, and then you have 10 publications in short time. Each of them building on a reputable and much cited dataset. So these paper gather good traction also.
I was at conferences where half the people just presented new datasets of gazes, pupils, fingerprints, smiles whatever. A lot of tedious work to build up, but it may be a good thing to build up reputation.
Sadly in the current times, reputation in numbers (citations, papers, etc) are sometimes regarded more worth then the content of these numbers.

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Changing University in First year of Phd
I just completed my senior year. I have been accepted to a grad school (say University X).
CASE A: I am quite familiar with the fact that one shouldn't change grad schools during a PhD. It is highly frowned upon and regarded skeptically. However my case is somewhat different.
I want to reapply for some PhD programs next year (fall). But, at the same time, I don't want to lose the only PhD seat I've got. So, I was thinking about whether I can go to University X this fall and apply for next fall (applications start this year's August).
If I get accepted, I would simply move to the other university. I obviously won't need any recommendation from professors of University X. It would be as though I had simply applied as an undergrad who waited one more year.
But my worry is, will this be considered as Case A? I am worried because if it is, then I may end up screwing up my relationship with the entire academia. When applying, I would be in the 1st semester of a PhD, which is not really a big deal. I wouldn't have any advisor at that point and would simply be taking a few classes.
Any suggestions?

Grad applications ask for your academic history. You're going to lie? We also ask your letter writers about you. You're going to tell them to lie?

I simply won't mention about the University X. Is that really bad ?

@zzz Yes, that's lying on your application. If you get in and they find out about it, they could rescind your offer.

What if I do mention about Uni X and still reapply ?? How is that gonna be looked at ?

one shouldn't change grad schools during Phd — [citation needed] I changed grad schools after two years. At least two of my former PhD students changed schools during their PhD, one into my department, another out. Nobody frowned, and nobody was skeptical.

@JeffE....I know about you (from your other posts). I honestly don't know how you did that but most people have discouraged me against this. It would be amazing if u can tell in detail,  how u did it ?

One key point: you don't mention anywhere in your question why you want to transfer.  Because you say "some PhD programs", I gather you don't have a specific other program in mind, and I can only assume that you don't have some compelling personal reason to do so (e.g. living in a certain city so as to care for a family member) but rather are simply trying to trade up.
Most students who enroll at programs which are not the top ones in their field would like to (or should like to!) move to better ones if they could, but because transferring programs is a fair amount of inconvenience for everyone, the threshold for doing so is rather high.  If you want to get into a better PhD program in year N+1 than you did in year N, then it would be reasonable to have a better application.
Trying to improve your application while newly enrolled in a PhD program is a bad idea.  First of all, as everyone else has said, of course you must disclose the fact that you are currently enrolled in a PhD program if you are applying to a different one.  The idea that you think otherwise is a bit alarming, not because this is such an evil thing to do but it shows how far away you are from understanding academic culture.  Do you think that no one will find out that you are currently in a PhD program?!?  Think again: likely all of your recommendation letters will mention this, for instance.
Moreover, the first semester of being a PhD student is a tough time to build your application: no one at your new program knows you very well (or at all), you haven't done anything much, and more than likely you are just absorbing the culture shock of a new environment and are not in a position to show superiority (and in fact most first year PhD students are fairly inept compared to other PhD students in the program: I know I was).  This phenomenon comes up when first year PhD students try to reapply for certain graduate fellowships (like an NSF fellowship) that they were also eligible for as a graduating undergraduate: they have to get a mix of recommendation letters from faculty at their old university who probably have nothing new or better to say about them than the previous time around and from faculty at their new university who have trouble saying more than "Mr. X is a student in our PhD program -- isn't he?  I'm pretty sure."
My advice is to do one of the following things.

Ask the university who accepted you whether you can defer for a year.  It is much better to ask this question up front than for them to find out later from someone else that you are trying to trade up.  It is a fairly good bet that you will be able to do it: I would much rather enroll a student a year later if in that intervening year they figured out that they really want to come.
Enroll in a non-PhD program either there or somewhere else: a non-degree program or a master's program.  In the American system, getting a non-terminal master's degree is essentially the culturally accepted version of the kind of academic laundering that you seek to do.  This is probably two years rather than just one year, and if you play your cards right you can actually improve your application and profile in that time.

Thanx for that idea about deferment. It can work. But, Can you apply to another school during the deferred period ?

@zzz: My understanding of deferment is that the student has the option, but not the obligation, to enroll in the following year.  I think the expectation is that a student who defers admission is not fully committed but is contemplating other plans.  So: yes, I think so, unless there is any specific information to the contrary.

......[http://academia.stackexchange.com/questions/44885/deferring-admission]

I don't see anything inherently wrong with changing PhD programs sufficiently early and with good cause. I do, however, find it wrong to be secretive and conspirative about it. In other words, you should by no means lie that you were previously (or currently) engaged in a PhD program at University X. Also, you should be prepared to answer the admittance committee why you are transferring. I would say, that "yours is a better program" is not enough, you should present a more compelling reason (i.e. a particular research interest and desire to cooperate with some particular faculty at the new uni) and be able to back it up.
You are probably worried what University X will do when they find out about your application. Well, chances are, if you are not assigned to a specific project with a specific mentor (you say you are not) or you don't receive any funding, they wouldn't care that much.
If you are worried, that if you mentioned University X, they would contact someone there to inquire about you, that could happen, even without a mentor.
In short, lying to the new institution is very bad and could hurt your chances tremendously. Deceit is usually (with negligible exceptions) the death sentence in academia. The new institution could even not only refuse to admit you, but also contact University X and tell them about your misconduct. Now that, would mean nothing but trouble for you.

Thanks.....So, I suppose, that means that I should mention Uni X. But, am not sure what to be done when Uni X finds out. I am in real pickle now.

What do you mean "when they find out"? You're going to need at least pne recommendation letter from someone at Uni X, which means you have to tell them that you plan to leave.

@JeffE....I will be applying for next fall i.e this august. My joining at Uni X is in this fall. How will I be able to get a reco from the profs in the very 1st semester ?

Getting a PhD from a decent institution takes lots of time and effort. Unless you are working on a project that highly motivates you the experience will be more difficult and unpleasant that it is worth.
If you don't feel compelled to devote an important chunk of your life to investigating a particular dissertation subject, then the Master's degree route makes a lot of sense. You should be better able to choose a research project after a year or two in an academic department.
You need to look for the best place to pursue answers to academic questions that will keep you motivated for the next 5-7 years. And if you get to the point where you are choosing advisors, don't fail to find out everything you can about them from their former students.
If you can honestly tell a recruiter that it is your heart's desire to investigate so-and-so with Professor X then that will make you a much more attractive candidate. You will be able to honestly say that because you will have read all his/her papers on some subject area and you can think of nothing else you would rather do than help find answers to the remaining open questions. Spending years in grad school to get a PhD without being properly motivated is a recipe for misery.
Good luck!

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Could a journal reject an article due to the style or quality of accompanying code?
I'm a student working on a doctoral thesis. We're working on a paper for which I've done most of the coding for the statistical analysis (the field is microbio/bioinformatics). I'm new to coding and the whole thing is more of an add on to my "real" career, which is medicine. Therefore, my style of coding is more than basic I'd say. Now I fear if we're handing in the manuscript plus the code to a journal for peer review it will be rejected or ridiculed. Is this possible?
edit: I use R to conduct a large statistical analysis. If someone would like to point out online learning resources, esp. for the fields of medicine/biology, I'd be very grateful.

"it will not be accepted or ridiculed" Accepted by whom? Your exam committee? Journal? Conference?

referring to a journal

I edited your question to clarify what you're asking, and also removed the research-undergraduate tag, as you say you're working on a doctoral thesis. You can change or undo my edits if they're not appropriate.

In my view, the editor can even reject the paper based on their mood on that day.

Discover codereview.stackexchange.com

you may want to have a look at the CRAPL license :p   (apologies for the RAS syndrome)

As a parallel, scientific results from a very messy lab wouldn't be rejected, but it may make reviewers/readers question the results (contamination, reproducibility etc.). However "hiding it " by not being open about the experimental set-up and design definitely wouldn't re-assure people that your results were good!

@David if we manage to publish, it will definitely be including the code. I don't want to hide anything, that was not part of the question

You will not have a paper rejected for poor coding style. Particularly not in bioinformatics. Unless the paper is a tool development paper, the chance that a reviewer even looks at the code is not that high, and if they do, it will just be to check that its reasonable. In the outside case a reviewer might spot a bug, or poor assumption that actaully makes the result wrong, but they will not reject you for poor style.
However, having the code associated with the paper massively increases the chances that it will be useful to someone else.

I agree a rejection is unlikely.  If they want any revisions you may be able to clean up the code then.

A lot of journals rightfully enforce release of the code. Results without the code to produce is not reproducible, not Science.

Absolutely they should and will check the code exists. But 90% of reviewers will stop at seeing the code is there. The best reviewer might check it more or less sensible, a tiny number might try to run it. None will critque the coding style. Note, this might be different for a tool/methods paper.

@Zenon That is not true, if the mathematics is described, the code is secondary and can be implemented and reproduced by others. The code is just a representation of some mathematical operations, not a magic oracle.

@Zenon, and in fact reproduction of the same results by the same mathematics in a different software implementation is the true reproduction. Just running someone's code on a different computer does not truly reproduce anything.

Let me bring up a more serious issue that you don't ask about. Poor coding "style" can also mean poor "coding". And poor coding can hide errors, affecting the results. If your research results don't depend on the coding then it may not be an issue and there is probably no need to publish the code itself, beyond some description of it.
But if the research results depend in any fundamental way on the code, as it does in some cases, then you are at risk and your paper may be rejected, properly, for having insupportable results. But that won't be for the "style."
I don't know which is the case here, but you need to assure yourself that your results are sound. You might need to collaborate with a programmer to provide suitable testing of your code, and perhaps improve it.

could you give me an example?

@mucl, an example of what? Bad code?

yes. Bc obviously my results do depend on my code. However, as I said above, I'm confident it works so far. It could just be a lot faster, e.g. I'm not used to creating loops in r.

Frankly, most code is bad even by professional software developers. And, writing code to analyze/simulate/take data has fewer demands to be 'good' and more to be 'good-enough'.

@mucl E.g., while (*s++ = *t++);, for an explanation, see: https://stackoverflow.com/a/7483682/3664487

Getting people to publish code in biology is a real problem, and this quesiton ere illustrates why. People are scared to let others see the code. The code generally run once code - that is it will never be useful for anyone else ever, and will almost certainly never be run again, but acts a log of how the analysis was conducted. It generally doesn't make sense to apply software engineering principles to it.

@Ian One of the main goals of "software engineering principles" is to allow code to be testable and correct. One would hope that that would be important. But given the general shoddy practices in many areas about reproducability and using tools correctly I'm afraid you're quite right in practice. That's how we end up with things like 1 in 5 of genetics papers containing errors due to excel reformatting.

If your code is df <- read.delim("data.tsv.gz") %>% gather("sample", "outcome") %>% seperate(sample, into=c("rep", "condition"));  t.test(outcome ~ condition, data=df), I fail to what a useful test might look like. This is a small exgeration, but much bioinformatics code is not, structurally, that different from this.

Your useful test is: an invented dataset in data.tsv.gz designed to create an obvious result derivable by hand or by inspection of the logic should, in fact, create that result. "Software engineering principles" are not just imaginary things like enforcing LSP or writing visitor patterns, it is also structuring your code (with or without formal methods) in a way such that it is easy to understand for someone looking at the code for the first time so that material logic errors are not covered by unnecessary cleverness or complexity.

@mucl: "It could just be a lot faster": for a one-off analysis that runs in a reasonable amount of time (i.e., less than a week?), this would never be considered an issue. Readability of the code is much more important (to make sure that the author really analyzed what they thought they analyzed!). Faster is only important if the current speed is "not fast enough to finish".

@Backgammon Super sure that there is no unnecessary cleverness hidden due to my limited skills

It could happen in principle, but only in extreme cases, where the code is so bad that it impacts the reliability of the results.
The code is a part of the research you are reporting on.  In some fields (e.g. parts of computer science) it is often an key aspect of the research itself; in other fields (e.g. most natural sciences) it’s a more auxiliary part of the setup, about analogous to the lab equipment.
Either way, it’s a part of the research, and so in principle, a paper could be rejected because if it was too bad.  However, “too bad” would have to be very bad indeed — typically if it had bugs that affected the results, or could have affected them.  (Just as a paper might be rejected if a referee found errors due to contaminated lab equipment.)  No referee will care about stylistic issues — the usual standard of most academic code is very variable indeed, and usually not very stylistically clean.

I would probably say that releasing the code is better than not.
In all likelihood the reviewer won't look at the code even if you include it, they may in-fact give you a little tick for including it even if they don't look at it since it would help with the reproducibility of your results by other people who do bother to look at it.
If they do look at it and don't like it there will be one of three outcomes:

They request more comments in the code
They say your code is not incorrect but it should be re-written for efficiency or style
They find a mistake in your code
I have ignored the case of them only running your code and not looking through it since it shouldn't give a different result when they run it compared to when you run it.

1) If they request more comments, fair's fair. Comments are important for readability, and in-fact you should make sure there are enough comments there now to make sure you'll quickly remember what you were trying to do with the code when you look at it in a few months time.
2) If they say you should improve the efficiency or style of your code then in all likelihood you can argue to the editor that only the code's results are relevant for the peer review, not the code style for your field. After that the editor will just ignore any similar comments from said reviewer. The exception is if they complain about your choice of variable/function names, which really falls more under 1) rather than 2). However if that happens then all that is involved is ctrl+f to find the bad variable names and give them a better, more explanatory, one.
3) The worst case scenario is they find a mistake in your code, in which case you can correct and check if/how this changes your results and modify your paper accordingly. The people who do this would probably include any reviewers who might try to reproduce your results on their own if they didn't have the code. In which case they may make different assumptions to you and therefore get different results which leads to a headache arguing over who's code is correct. Since they have your code you can now challenge them to point out the mistake if they just say your results don't match with my results.
Now it is possible that you will find nothing of interest after making this correction which makes it seem like all your work in the project was for nothing, but its important to remember you would have done all this work and written/verified your code before reaching this point, so in fact all you've lost is the time taken to write the paper, which while not good is still a learning experience for you so the next paper you write is done quicker/better. Furthermore it means you don't have a paper that is incorrect and leading to confusion when people try to replicate/extend the research that is tied to your name.
While this case sounds very bad it will only occur if your code is wrong. If you are confident in your code then its fairly safe to exclude this case, if you aren't confident in your code then you should check it until you are.
One last thing that you should keep in mind is that if you release your code you will want to provide a license with your code without the license nobody has a legal right to use it/extend it/write code based off reading your code. Or at the very least this falls into a gray area. Normally scientific code is released with a very open license (I think MIT license is the standard) but you can google to find out what types of licenses there are.

It sounds harsh but I sometimes used to cringe at the rats-nest of code some scientists would ask me for advice on.
If your development of the code has been linear rather than cyclical then I would bet my boots it contains significant errors.
A problem with R is that a lot of it is created by amateurs.
Compare this with the various libraries of cast-iron copper-bottomed (professional) routines that have stood the tests of time - the problem is of course licensing fees.
If you wrote your own statistical code then I suggest two ways forward:

Put aside your original code and rewrite it again from scratch with the benefit of hindsight. You will write it much quicker and much better the second time. When finished, run it on the data and see if you get the same results.

or

Get hold of proper tested routines and write a simple program around them. For example  NAG routines. https://www.nag.com/content/using-r-nag-library

If the professional packages cost too much then find out if someone else has a license they will let you use as a temporary measure.
Or pay a keen undergrad to write the new code for you. Test theirs against yours.

Given the OP's statement of the problem, I sincerely doubt they are writing their own mathematical algorithms or packages to analyze their data, as is implied in this answer. I'm fairly sure they wrote a long script that maybe uses several packages. Whether "professional packages" are actually better than open source packages is a whole different debate that I won't restart.

I am a software developer.  I frequently work with research scientists, incorporating their equations and simulations into other programs.  I originally had your same concerns, but from the other side (worried it would be detrimental that I only have a low level of knowledge about the underlying science).  Someone explained to me that it was like learning a new language.  To a native speaker, yes, you'll be harder to understand.  It means a lot, though, that you're even making an effort to learn that language.  People know you're new at it and they'll generally cut you a lot of slack.
Like you said, you're in the medical field.  There's not an expectation that you're proficient in coding, or Russian literary history, or accounting, or anything else that you haven't been trained in.  Research papers get published all the time that are clearly not in the author's native language.  The writing is rough and hard to read, but the paper still gets published because the science is sound and that's really what it's all about.  Your code is really no different.  Unless your code is so bad that it makes the paper harder to understand or that it has bugs that cause incorrect results, I highly doubt anyone would think any less of it.
If you're really concerned about the code's quality, create a public repository on GitHub (or similar) and invite others to help clean it up.  You might be surprised how much your code can be improved with nothing more than a half hour and a different pair of eyes.
As an aside, I've had a number of my scientist co-workers apologize for the quality of the code they give me.  They're shocked when I tell them that their code actually looked better than the absolute garbage that some professional programmers generate.  The very fact that you can see quality problems in your own code says that you're more skilled at it than you realize.

Bad coding style can lead to reviewers not reading the code. They usually are not obliged to read it and especially not to review it, but providing code can help to get good reviews because they are able to reproduce your results, which is a good thing.
I would say the most important thing is technical correctness, followed by an easy way to run it (try to use easy build systems and provide instructions for dependencies, when it is complicated to install them and maybe provide binaries in addition to the code).
Coding style comes last and many academic codes are not so easy to read. Especially mathematicians tend to use a lot of non-descriptive one-character variable names, which can only be understood when reading the corresponding paper at the same time.

You seek to balance the time and effort to develop the code to a degree that it is

«good enough» to tackle the task you currently address in comparison with an earlier defined set of duties
easy to maintain by you or (future) colleagues in your group / community, e.g. to add features you did not anticipate in the beginning
documented well enough that others not directly interacting with you may understand how to use the program and its inner working

while programming not necessarily is your centre of activity.
In your context, I recommend programming classes specifically set up for an audience without prior exposure to computer science.  Here, software carpentry is the first site which comes into my mind.  Because of its collaborative character designing the courses (survey, includes R), their classes exemplify best practices and standards you may use as a reference which suits places around the globe they taught and teach. It  equally may introduce you to peers of similar interests to yours, too.  As a result, your code quality improves and is more likely to be accepted by others.
Contrasting to on-line classes on sites like edx.org, improvements of their material is not constrained to the duration of the class itself. Any interested may access their public repositories and suggest improvement.

authors: Vladimir F Героям слава

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


text:
How to cite self-created images or pictures in thesis
When we put some images in a thesis, we provide a reference to its source where it’s located. If I have created my own images or pictures, how do I make it clear that they are my images and I did not copy and paste them from somewhere?.
So here is the scenario. I am comparing my application architecture with the existing architecture. Since it was a literature study, my architecture is quite different except for one or two components that share the idea with the other one.  I am showing both architectures. I explicitly mention the source of the other. But what about my own?
Is there a need to cite self-created images? If yes then how to cite them?

Have a look at the relevant guidelines/rules at your university/department.
Where I am, one typically signs that everything that is not your work or that is not novel is cited. Novelty in the thesis context is defined as "has not been used in any other exam/thesis". Papers published as part of the thesis work do not hamper thesis-relevant novelty at "my" university. But since it is up to the unviersity (or even faculty) to decide their exam rules, you may be subject to different rules.
In addition, copyright plays a role. You may be author without having the copyright. The holder/owner of the copyright can allow you to re-use images but stipulate certain ways of citing.
Anything (images, diagrams, tables, text) you created for the current thesis (so they are  novel according to the thesis rules) and where you hold the copyright (so no rules binding to use particular citation forms) are not cited. If there is no citation, you claim it's yours and novel for this thesis - and thus that it should be included in the content based on which your work is judged by the thesis committee.

In my case, I needed to cite my own work only if/when:

I wanted to reuse an image/diagram that I used already for an earlier thesis or exam, e.g. had I wanted a diagram from my Master thesis to re-appear in my PhD thesis. In that case, I'd have cited my Master thesis like unrelated work. Unrelated since this is not part of the work the committee should judge.

I transfered copyright for several papers I authored to the respective publishers. They typically did allow re-use in theses but prescribed citation sentences like e.g. "This image is reused from [CB3] with kind permission of $publisher." [CB3] would be how I cited e.g. the third paper I wrote as part of PhD current thesis.
Had I retained copyright (non-exclusive license to the publisher), I wouldn't have need to cite this way. Nevertheless, I'd still think it advisable to tell the reader that this diagram can also be found in that paper - it saves people from trying to find out whether the paper contains anything in addition to what the thesis contains. Similarly, I could have used [3], i.e. there was no requirement to make the citiations of my papers for the thesis immediately distinguishable from other citations, but I thought it a good idea to provide such a distincition - e.g. because it makes it clear to the committee that this is part of what they judge as my thesis.

For your scenario of diagrams illustrating some application architecture described in some paper:

if the diagram for the existing one is directly taken from the paper, you apply for a license to re-use that image with the publisher and then do whatever they stipulate in this license.

if you draw your own diagram (in your architecture diagram "language"/style) from the description in the paper, you cite the idea/description, e.g. "diagram of architecture described in [27]" but the diagram itself is your own work, and novel and original part of your thesis.
With "your own diagram" I mean e.g. situations like: They have some diagram in the paper. But their way of illustrating isn't really suitable for your thesis since you need to highlight/contrast aspects that are similar to|differ from the architecture you developed. You therefore make a new graph that describes their architecture in another language/style that allows to depict their architecture as well as your architecture.

Your diagram of your architecture is original and novel work that is part of your thesis. No citation here, unless you signed away the copyright for this diagram - in which case you need a license by the new copyright owner (= journal publisher). In which case you do whatever the license says you should do.

really helpful. I just wanted to avoid any ambiguity about the components. we are both using the same component because we have to. Its the component provided by the technology to use however we can. I just wanted to avoid that I stole the idea just because the name of the components are the same and function in the same way. but that's their job to provide this functionality

There is no need to cite self-created, previously-unpublished images any more than you need to cite self-written, previously unpublished words.  By absence of a citation you are claiming the work as your own.
Since this is for a thesis, you should probably check with your advisor / supervisor to be absolutely certain they share that view.

You may be asked to document the sources of figures in your thesis as part of the process of submitting to ProQuest or other repositories.  If that happens, just state that you created these images yourself.

Cite your own work just like you'd cite someone else's. Without citation you're suggesting originality.
A reader knows when an author cites their own work. The author of both works are the same (or overlapping). There's no need to be explicit (by stating, for instance, in my earlier work), unless it is useful.
For works derived from a thesis (as opposed to published works), there isn't an explicit need to self-cite, since works derived from a thesis are considered original, they haven't been published before. That said, you might want to mention something along the lines of: My thesis contains a preliminary version of this work, or similar. (You'll need to adapt slightly when you aren't the sole author.)

kindly check my updated question to understand the scenario

Aren't the first two sentences in direct contradiction? You say to "cite your own work". Then you say "A reader knows when an author cites their own work [...] there's no need to be explicit", which I take to mean, "you don't need to cite your own work."

@user91988 you don't need to cite your own work isn't my reading, my edit clarifies.


text:
How can I recover professionally from being a crank?
Three years ago I got kicked out of graduate school in physics. I was suffering from mental illness, which led me to believe I made a huge discovery in physics. But my advisor kept saying that what I was doing is nonsense and that I should focus on something else. I just ignored him and kept working on huge discovery, convinced I was going to win a Nobel prize.
I started sending many emails to many physics people (I had a list of thousand email addresses I found online) hoping someone would realize my amazing discovery. I got kicked from school which made me send more emails (almost one a day near the end), and when I got negative responses I sent an email to everyone on the list insulting them and saying I deserved to be in their place.
I got psychiatric help, and eventually doctors found a brain tumor, which they removed. I am now taking drugs, and doing much better. I now realize how insane my behavior was.
I want to re-apply to grad school, but I’m scared people will recognize my name or contact my university. My undergraduate grades were very good. Should I mention my illness (with proof) when applying? Should I send apology emails to the people I’ve contacted?

For context, since admission systems vary around the world, what country did you study in, and/or in what countries would you be applying?  For the US, for instance, I would emphasize the importance of letters of recommendation from former professors who can attest to your recovery and ability to do reasonable work going forward.

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Great title ! :-) . Good luck in your endeavours. I once encountered the opposite where a brilliant student just short of completing their PhD sustained a brain injury in a car accident. I acted as an "expert witness" in a small claims court and could not understand his devious behaviour until I discovered the background. I'm pleased for you that your journey has been in the positive direction.

From Feynman: "You are under no obligation to remain the same person you were a year ago, a month ago, or even a day ago. You are here to create yourself, continuously."

I am very curious to see how things went for you!

A few suggestions:

If it were me, I would be very forthcoming about the illness. Of course, no one is entitled to your private medical information, so you will have to decide what you're comfortable with. But "an undiagnosed brain tumor caused me to act erratically" is a very convincing explanation, and does not reflect poorly on you.
Consider reaching out to your previous advisors / colleagues. Even those who were furious at your previous behavior would probably accept that an undiagnosed brain tumor caused you to exhibit poor judgment. It's a "Dr. Jekyll and Mr. Hyde" situation.
Along similar lines, consider contacting the university, and the specific school within the university, to discuss whether the expulsion can be expunged or converted to some other classification. Most universities are really understanding if you speak to the right people.
When you apply, I would absolutely explain what happened. I would give a shorter version of what you wrote above -- even if they don't recognize your name, they will see that you were expelled, so it's better to tell your story. And you did a good job telling the story above, so I trust that you can write an explanation that is similarly clear and compelling.
There will likely be no need to provide medical proof. You could (perhaps even should) offer to provide proof, but I suspect most admissions committees would not request it. Among other reasons, it will likely be clear from your tone that you have recovered.
I don't think it's necessary to send an apology to your entire mailing list. But I don't think doing so would be inappropriate either. If you do so, be concise: no need for more than a sentence or two.

"It's a "Dr. Jekyll and Mr. Hyde" situation."  I guess you have not read the book.

haha, I suspected I was messing up that reference. I actually just purchased a paper copy of it this week, which is probably why it came to mind. But as you can tell, I have not started reading it yet, perhaps this public shaming will inspire me :-)

There is no need to provide medical proof. In light of the erratic behavior, I'm not sure how many people would buy a seemingly outlandish excuse of a "brain tumor" without some amount of proof. I imagine many if not most researchers who recognize the name will simply disregard any explanation. It will be an uphill battle. On the other hand unless OP's name is particularly unique there's a chance that they won't be immediately recognized.

I disagree; most "cranks" would not be able to put together a respectable application package, nor to characterize their previous behavior as "insane." That OP has done both suggests that the story is true. The only place I could imagine asking for proof is if OP's former grad school wanted to readmit them outside of the normal channels; they may need some justification for bypassing the normal channels.

I agree that no one should need proof, but also wonder how skeptical people will be.  As the OP is obviously open to sharing, I would suggest a possible middle ground: Show the former advisor.  He is a key ally in any event.  And the more fully convinced he is, the more effective an ally he will be.  It would also be good to share with the advisor those concerns about having alienated others the advisor may not have known about; he may even be proactive in convincing colleagues the OP has recovered

@NDEthos if not expunged then certainly it is possible to change the status from “expelled” to “withdraw” retroactively after someone from the university has verified the broad outlines of the story.  Likely an appeals committee of some sorts deals with this kind of exceptional situation.

+1, also to explaining it was cancer. An unspecified “mental illness”, even if cured, might face more stigma.

I wouldn't send an apology to the mailing list - I don't think OP should really have kept the mailing list.

I strongly suggest that the last point specify that an apology email should have a clear title such as "I wish to apologize", so that people will not immediately assume it is a spam email based on their memory of that sender address. @DavidW: I agree with cag51 in that I don't think it is inappropriate to do it concisely. The reason is that I feel this is basic courtesy; if in the past I did something wrong to someone (such as wasting their time or insulting them or spreading fake news), I should make sincere amends (while minimizing the time they would need to process my apology).

I agree with all but one point: I would definitely send a proof along with each communication on the matter. If someone told me "hey, I was #@! back then, but it's not my fault, I had a brain tumor, so please let me in into your company/university etc. again", my first reaction would be "yeah, sure..."

Follow-on to user21820's suggestion: Also, don't send the email from your existing email address (and perhaps even full name) which has (have) probably been designated as a spam source by many.  (Too late for the OP's initial email burst, surely.)

Change your name
I don't know about other countries but in the UK one can change their name by deed poll. https://www.gov.uk/change-name-deed-poll
It is also acceptable to write academic papers under a pseudonym. If I publish under a pseudonym, can I still take credit for my work?
Also in the UK, universities are required to take issues of mental health very seriously. https://www.universitiesuk.ac.uk/policy-and-analysis/stepchange
If you did very well in your undergraduate studies, I suggest you contact lecturers who were kindly disposed towards you then and ask if they will help by providing references. Remind them of your record (get a transcript) because, if at that time you were an 'ordinary' student they may not remember you. If they got word of your "craziness" they will only have heard it second hand.  Tell them about your brain tumour and its removal - no need to mention follow-up drugs IMO.  Remind them of how you were when they knew you and ask if they will support you on that basis.
Once you have been formally accepted at a new university, now is the time to notify them of your legal name change. The paperwork will go through the office.
How do I know this? I actually did the name-change thing. I didn't do what you did in terms of mental health, but for personal reasons I wanted to leave my old life behind (see note). No-one but my family and a few old friends know what my name used to be.
If you are not in the UK then of course you will need to research the situation in your own country. (or apply to a UK university)

Note: Don't worry, nothing criminal!

Wikipedia summarizes name change policies & law in various places.

Before changing my name, I'd try to switch the subfield of my research or try my luck in corporate research. Changing one's name will lead to questions from the environment (friends, colleagues, family, future partner), which were not aware of being a crank in academia.

Seems a bit extreme, but might help.  I'd be interested to hear what happened to the OP

Congrats on identifying and moving past  your illness!  You'll find academics a comparatively accepting crowd as you move on.
I would suggest contacting those you've "cranked" to, telling them exactly what you've told us.  You had a brain tumor,  and it's been removed.  You're embarrassed by your behavior during your illness, though not apologetic, as people don't need to apologize for being ill. Tell them future contacts from you will be in only professionally appropriate situations, and request that earlier contacts be evaluated in appropriate context.

I think it's definitely reasonable to contact the people most intimately involved - definitely the past advisor and likely other colleagues at that institution including those who were involved in their dismissal, thesis committee, etc. But I would be far less sure about contacting the potentially thousands of people who were emailed...(an apology to a listserv might be an exception, I wouldn't really consider that to be an email to thousands).

In this specific case, If you do contact those people, I think a form letter might actually be significantly better than a personalized one. If I got a personalized email from someone who had been a crank in the past (and whose behavior I might have perceived as threatening, in particular), I would tend to be concerned. But if I were BCC'ed (NOT CC'ed, make sure to know the difference) on a general apology-to-all email, outlining the story above, it would feel more similar to getting it through a mailing list -- it would not feel threatening if it's clearly not directed at me personally.

... although, as a counterpoint, the mere act of contacting a huge number of people who may not want to be contacted is itself a crankish behavior. So perhaps better to limit to to the listserv and to specific people who need to hear it, and let the news diffuse through the grapevine to the rest.

Since the release of the movie A Beautiful Mind I'm certain that a lot of academics have seen it and can understand that mental illness can happen even to the most brilliant people.

The story begins in Nash's days as a graduate student at Princeton
University. Early in the film, Nash begins to develop paranoid
schizophrenia and endures delusional episodes while watching the
burden his condition brings on his wife Alicia and friends.
https://en.wikipedia.org/wiki/A_Beautiful_Mind_(film)

If you haven't seen it yourself then I recommend it as a confidence booster. This true story shows that it is still possible to be successful despite having to cope with major delusions.
With regard to apologies/explanations, I think the people who need them most will be those you know personally. They know you by sight and will recognise you at conferences. A short but sincere apology and explanation is all that is needed.
A possible title for an email might be, "Apology from  a student who was ill". The body could simply be: "I would like to apologise sincerely for an email I sent you when I was suffering from a brain tumour. It caused me to have delusions. Thankfully surgery has corrected this and I am planning to resume my normal life in academia. Once again I apologise for any offence I may have caused."

+1 Professional recovery is possible, I know someone who acted like a maniac at work due to (hormonal) cancer treatment. After it was all behind her, she was a valued and respected colleague. I honestly wish the OP all the luck in the world.

Your case is very special and not something one encounters usually. So I doubt an accurate and confident answer is possible by the community here.
Bad things happen in life for everyone. In your case, you are out of it. And that is positive. Your past actions definitely will have an impact on your life and career but you should note that memory of people is dynamic. Your present matters more to your future than the past. And you have a very good and honest reason for your actions in past.
I do not think you need to apologize to each and everyone except the people who you have an in-person connection with. Definitely to the people in your previous school. Others would have forgotten you already. Change your email-id. Start fresh.
You are not a crank anymore. That person is cured and you are different. Mention this in your application. I am sure that you will eventually get a good PhD school, and who knows, might win a Nobel prize.

Unless you were previously known to them or legitimately made them anxious for some reason, most of them will have forgotten your name. (If we are talking about a few-year gap.) It's normal for a crank to get offended when their idea is shot down, it's only when it turns into extended harassment that it becomes noteworthy. If someone told you about a perpetual motion machine a few years ago you might remember it but probably not their name.
I have gone through something similar to you (I know how priceless your recovery is and I know that the subtle stuff takes years to mend). Here is what I would tell you:
It's a war story, not a sob story. You've learned a lot that many people never will. There are lots of interesting things you could tell; you have, I'm sure, learned a lot about the mind and soul, about human behaviour. This sort of thing can help you be more successful because you have more insight into how other people's minds work. "Own" your past behaviour—show why it's interesting rather than apologising/showing how "you're better now"/are safe to be trusted. You can use humour to lighten it up, but intellectual people often want to learn more about the hows and whys.
People are prejudiced about mental disorders. Unfortunately. I've noticed subtle changes in first impressions if I speak freely to people. Now I understand what "covert racism" is. People treat you with respect but somehow you get far fewer follow-ups to the proverbial résumé.
Once people have formed a relationship with you, hearing your story actually makes them gain respect for you. But don't volunteer too much too early is my advice.
Nothing says "sane" like face-to-face. If you meet someone in person and they get the impression you are a normal, intelligent person, this carries a lot of weight over any written or word-of-mouth communication. If you want to start on the right foot with someone, try to catch them at an event, or better still, have someone introduce you. (Dammit, COVID.) I'm not saying this is guaranteed but if you want to apologise to someone, and you have the option to do it in person, do that.
Find the language. For unusual experiences like this, it's hard to find the right words. It's easy to fumble or say nothing, which leaves people confused or making the wrong assumptions. I had to learn to say "oh, sorry, I got overexcited, that's embarrassing" and "sorry I'm not feeling well right now." Sometimes it's about spin, for example "I became obsessed with an idea that wasn't very good" compared to "I had an idea that was utterly insane and acted like I had just discovered one of the biggest breakthroughs ever." I'm still not very good at this. I like to tell my story from my perspective, when the "objective" perspective is probably better most of the time.

I am confused about your fourth paragraph. What point are you trying to make?

I'm sorry this happened to you. I too suffer from mental illness, and sometimes people just don't understand.
I would explain what the circumstances were behind your episode. People will be very sympathetic when they realize that a tumor in you brain was the cause. Even those you insulted will understand.
Do not change your name as some have suggested. That makes it seem as though you are hiding from what happened.
Do not contact the 1000 people you emailed. If you feel that you want to explain your actions to specific people, then do that. If you got into an exchange with a specific person, maybe get in touch with them and explain. I'll bet that the majority of the people on the email blast you sent out have forgotten your name and/or never opened the email to begin with.
Move on with your life. Continue your education. You didn't intentionally lie or try to trick people into a believing a sham theory. You had a brain tumor. Again, people will be very sympathetic when they know the reason behind what happened.

You self-identity as a recovered crank, which is unusual. But then, you had a specific medical cause perturbing your thought patterns and you now have a competent professional perspective on your erstwhile cranky notions (and the accompanying megalomania and paranoia), something which typical cranks do not ever acquire.
Cranks also, according to expert Underwood Dudley, never sent out messages stating 'I have stopped now.' You are considering such. People that you might have pestered repeatedly, and to whom you perhaps made angry comments or veiled threats (as cranks often do), would probably appreciate an apology/explanation. People who were probably able to summarily dismiss you as 'just another one' probably do not need to hear from you again.
To your question. As a former director and admissions tutor in a large MSc/PhD research school, I would assess your current state of competence and base my decision on this, regardless of any history and whether I knew about it. If you did not disclose it, but I found out about it later, I would be somewhat miffed but could easily forgive you if your performance was stellar, much less so otherwise. So choosing to keep this to yourself (which despite of what I just said I do think you'd be entitled to) would be a bit of a gamble. If you do not disclose but still exhibit, at interview, signs of mental frailness (shyness, insecurity), or its diametrical opposite, that would worry me in its own right since the programme is demanding. If you do disclose I would worry about the possibility of a relapse (yes, I am aware it was due to that tumor but human psychology is complex) and at the very least address this with you and work out a sort of 'early warnings sign' protocol for us both.

Nobody on this site should be advising on your recovery from illness.  Discuss that with a professional who has examined you personally.
If you apply for a new PhD, you will be required to give a record of your previous studies.  This will show you were "kicked out."  To convince an admissions committee you should be readmitted, you will need to tell them your expulsion was related to an untreated illness and you will need to inform the committee of the degree to which you have recovered from the illness and probability of recurrence (ask your medical professional).  You do not need to provide proof of the illness, or even say what it was.  You should explicitly state that the illness caused behavior which lead to expulsion.
Any educated person who read your emails would have realized you were ill.  Apologizing would be a matter of personal preference.
Based on the limited information you provided, I do not see any reason why you could not get a PhD.

I think the first sentence is a bit unfair - the OP didn't ask for any medical advice, only career advice.

@DGreenwood Your comment is unfair.  The moderator removed the ambiguous title at my request.

Perhaps the point being made here is that with a mental illness context, career advice is not completely independent of medical advice.

No, the point being made was that originally the question title could have been interpreted as asking for medical advice.  It was changed.

@AnonymousPhysicist if your answer addresses an older version of the question and isn’t pertinent to the current version, you should delete or edit your answer rather than complaining of unfair treatment when people think you’re not making sense.

@DanRomik It's reasonable to view the edit history once before casting judgement.  It is unreasonable to edit an answer an unlimited number of times because a question was edited an unlimited number of times.  Thus I never do as you suggest.  Also, the advice is still correct.

I was more intending to point out hypocrisy rather than complain.

Being a "crank" is not a medical condition, it is a professional faux pas. OP never asked "how can I recover from my brain tumor" they asked "how can I recover from being a crank". Adding "professionally" in there makes it super extra clear, but I see no reason to interpret crankdom as a medical condition in the title, nor did the body of the post ever suggest OP wanted anything besides professional advice: they asked about mentioning the condition in applications and apologies. They also mentioned clearly that they have been under medical and psychiatric care.

It also seems a bit rich to me to refuse to edit an answer based on a request you specifically made to edit the question (and which you could have done yourself). If you thought the question should not have been answered in the original form, you should not answer the question.


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Publishing a physics paper when you are outside academia?
I'd like to publish a paper in a cosmology journal. However, I've been outside academia for about 3 years since completing my masters. Is there any platform where I can share my idea and get feedback to beat it into shape? Or where it can be critically judged? What is the best way to proceed to get this published?

What’s wrong with the standard way of just submitting to a journal?  The feedback (and critical appraisal) is in the form of the referee reviews.

I've heard there's a money barrier. Not sure how much though :/

There are plenty of good journals that do not charge publication fees.

I see ... thanks. I was not aware. Thank you

Can't you post it on arXiv ? People might read it and comment.

Do you have any publishing experience?

Possible duplicate of https://academia.stackexchange.com/questions/101/how-do-you-judge-the-quality-of-a-journal

@Wrzlprmft nope

What's the topic of your work? (I'm a cosmologist so professionally interested. If you want to drop me an email my contact info is linked in my profile here).

@astronat sent an email. Thank you so much for showing interest.

To answer your question: yes of course it's possible to publish a paper if you are outside of academia.  However I would like to make the following important comments.

Even if you'd like to publish a paper, there is no guarantee that your work will meet the quality threshold of any one journal.  It's not a matter of "liking" to publish stuff (everyone would like to publish a paper), it's mostly a matter of meeting the quality requirements, and meeting these requirements has (in principle at least) nothing to do with holding an academic position.
It is often easier to meet the quality requirement if you are part of an active research program, simply because you are more likely to be current with the topical literature and have better context to judge if your work is actually novel, and more likely to have experience (or access to experienced collaborators) at presenting your results in a matter that will be of interest to the readers of the journal.
There are no obvious platforms for discussion of results that need to be "beat into shape".  Most of the work is expected to be "publication ready" rather than at a stage where it requires to be "beat into shape."  Unless your are exceptional or have lots of experience, properly editing and "beating into shape" is usually done through collaboration so maybe the first step for you is to find a collaborator with experience in the field.  Finding a collaborator is a highly non-trivial task.
There are many more disreputable journals that will charge a fee than reputable journals that will not.  There are of course some excellent journals that do charge as many work on an open-access model.
There is no monetary cost (that I know of) in submitting to a journal that would charge a fee, although you want to be careful not to transfer copyrights before the work is accepted.  You could try to submit to an open-access journal but your cover letter should indicate clearly your circumstance and that you do not have funds to pay any author charges: the journal might still continue with the referee process and waive the author charges, but there's no guarantee of that.

If a journal charges a publication fee, and one does not intend to pay that fee, one probably should not submit - the "cost" is goodwill.

@Allure Agreed it’s a long shot but as with many things some journals will make exceptions.  Editors do have some discretion and can recommend waiving the fee, but the authors would usually need a compelling reason for this.  I would certainly expect authors to clearly make their case in their cover letter.

Certainly post the paper on the arxiv, to give it some exposure and potentially get some feedback from strangers in your area. Consider sending it to some contacts you had in academia without the expectation of a response, knowing that they are very busy and may not be able to read it. Please understand that, especially if your paper claims a particularly groundbreaking discovery, or if it is not written exceptionally well and in proper style for publications in your field, it may very quickly be dismissed. Once you are confident in it, feel free to submit it to a journal without reviewing costs, and you will get feedback from them directly, one way or the other.

… not clear it would post on arXiv since the submission requires a registered author or an endorsement, both of which appear unlikely at this stage.


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Does the typesetting process start all over again after submitting the correction of the proofs?
I have received the proofs of my article a week after acceptance. There were some mistakes made during the typesetting which I have outlined while correcting the proofs. It's been a week since the corrections were submitted. My question is:
What happens once the corrections are submitted? Does the process of generating the proofs start all over again, and hence one should expect the same amount of time as between acceptance and receiving the initial proofs to pass before the manuscript is published online?

With modern equipment, no, the actual typesetting won't be started over and the actual time allocated for the job is likely quite short for a few corrections. Things are automated these days. Manual checking is still required though - end of page and line, ect.
But the job has to be scheduled and the business process may put the paper at the end of a queue so that the overall time that you experience might be longer than you'd expect.

Things are automated these days Is it possible to automate corrections? I'm under the impression that the corrections are provided in a form that's not machine-readable, so implementing them is still a manual process.

@Allure, true enough, but the "typeset" is now likely (very likely) an electronic document, not cast lead as was once the case. Only the changes need to be incorporated and the overall effect judged and fixed when needed (widows and orphans, for example). Margins and flow are almost certainly automated. Even hyphenation when needed.

@Buffy Though a recent question was about the use of LaTeX for books on reddit/LaTeX, one may speculate scientific journals do not differ this much in technology here. One of the answers noted XML as one tools among others for tailored typesetting by letex, one company more frank about how data by their clients are processed (SpringerNature, Wiley VCH, de Gruyter, Thieme are mentioned explicitly).

The bulk of the work - when references are fixed, figures are positioned, imprints are added, margins are modified, etc. - is done during the first proofs. That's why the first proofs are often very different from the accepted manuscript.
After the first proofs stage, any changes will usually be minor typographical fixes, which are easily incorporated (unless they cause text to overrun, but it's rare for these overruns to be severe enough to make text run between pages).
Second proofs are usually faster than first proofs, but there is some scatter in the time needed since, e.g., the journal staff may be accelerating another paper which has been marked "urgent". Order of magnitude estimate is "a few days".

The journal staff might have many papers, actually. It is hard to predict or even to know their process.

one should expect the same amount of time, as between acceptance and receiving the initial proofs, to pass before the manuscript is published online?

No, in my experience it is much more random than that.


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Why do some papers not have a DOI?
When I cite papers online, especially in Wikipedia pages, it is very convenient to use their DOI. However, some papers which I would like to cite (like this and that) have no DOI. Or at least, I haven't been able to find their DOI in the crossref search form.
Why isn't a DOI assigned to all papers? Is there something I can do to change this?
EDIT: I now found out that in ResearchGate, I can upload my paper and it automatically receives a DOI. So practically, my problem is solved.

Perhaps because it typically costs some amount of money to register a DOI with a registration service?

The question is skewed by your asking it in the passive voice. Why doesn't who assign a DOI to all papers?

ResearchGate's instructions https://explore.researchgate.net/display/support/Generating+a+DOI fail: there's neither a "timeline" tab nor a "Generate a DOI" button.  So how did you accomplish this?

Ah.  ResearchGate elsewhere says "Publications of type 'Article' and 'Conference Paper' are considered to have been published elsewhere, therefore, DOIs cannot be generated for this publication type."

A process exists for obtaining DOI's, including the submission of meta-data and fees.  Thus, it is time and cost prohibitive for some authors / publishers to obtain DOI's for their published works.
You can find information about DOI's here: http://www.doi.org/faq.html

Can an author request a DOI for his paper if he pay all the fees himself, if the journal/conference do not request it at all?

The purpose of a DOI is to have a web link to a permanent archive of a paper. Unless the author is planning to maintain that permanent archive, it would not make sense for them to request a DOI on their own. @EnthusiasticStudent

@OswaldVeblen's answer about making that commitment to keeping the DOI 'maintained' is a big part of the picture. The reason that DOIs were adopted was their 'persistent' quality. CrossRef has a two-way agreement with publishers who commit to updating the link metadata (where the DOI points to).

DOIs are assigned by CrossRef on behalf of members. CrossRef is an association of scholarly publishers, so the members are therefore publishers rather than authors.
DOIs were introduce because of "link-rot": citing a paper by URL and within 6 months the URL doesn't work. When a publisher joins CrossRef they make a commitment to keep the DOI link metadata updated, so the DOI always points to the paper if, for example, the publisher is bought out and all the URLs change. This agreement is an important part of the DOI system and explains why publishers are members rather than authors.
Assigning a DOI is normally done during the process of publication, and will normally be done automatically. That's not to say that DOIs can't be assigned after publication: DOI 10.1098/rstl.1672.0051 is for a paper published in 1672. Publishers generally assign DOIs to new content but not to back files because new content is more likely to be cited.
It's not free to register a DOI, off the top of my head, around a dollar per DOI. It's normal (and cheaper) for publishers to deposit back-files, i.e. for publications older than 2 years (again, off the top of my head).
So, if you want to get a DOI assigned you can go to the publisher and request that they register a CrossRef DOI.
STM (Science Technology and Medicine) is a very fast-moving field with lots of papers published and cited. Humanities publishing tends to move at a different pace and tends to have different priorities. Therefore you may find STM publishers more likely to assign (and to need to assign) DOIs than in other fields.
The alternative is that you get a DOI from another organisation, for example FigShare. There are examples of people registering FigShare DOIs for their publications.
CrossRef was created to solve the problems of assigning persistent identifiers (DOIs) and linking between papers (one DOI cites another DOI). CrossRef also has lots of other infrastructure, such as bibliographic metadata, FundRef, CrossMark, metadata API etc so it's the best place to register scholarly publications.

Disclaimer: I work for CrossRef

So how come some DOIs point to e.g. a pubmed entry? wouldn't it make more (financial) sense for the publisher to directly link to their site?

Do you have an example of a DOI pointing to a Pubmed page?

Nvm I think my reference manager tricked me. I scraped a reference using only the DOI, and it found a pubmed URL. Turns out it didn't resolve the actual DOI as I thought it would. But since pubmed often seems to offer multiple options for downloading, wouldn't it be a good idea for a DOI?

This answer almost makes it sound like CrossRef created the notion of a DOI, which is quite misleading. DOIs are an international standard via ISO. See https://en.wikipedia.org/wiki/Digital_object_identifier

This wasn't meant to be misleading. Crossref used DOI to implement persistent identifiers. Note that the ISO standard is 2012, Crossref was founded some time prior.

A DOI is registered by a so-called Registration Agency (see FAQ  1 and 2 at DOI). Since there is a cost associated with the service, it may not be feasible for all to add such identifiers.

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


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mailing list for local conferences
Often I learn about conferences, even in my own country, when it is too late to submit papers. Is there a mailing list, or another way to get information about conferences in a specific location and domain?
EDIT: I am mainly interested in computer science and game theory.

Many fields have mailing lists (listservers) to distribute information. To help you,it would therefore be necessary to know your specialization or general field. There is no service that would safely provide information for all research fields.

You can use http://www.conferencealerts.com/ to locate academic conferences in your desired country. These listings are sorted by a topic or country which you can select on the first page. Once chosen you will get a list of the various conferences organized by month. Moreover, you have the option of subscribing and thus receiving email announcements about those events.

ConfSearch does something similar for Computer Science conferences.

There is a wiki devoted to call for papers (http://www.wikicfp.com/cfp/).
Googling can help you find earlier editions of conferences and so forth. Make a list of the ones relevant for you and when they occur – each edition of a conference will occur at the same time of year. Keep this list on your wall, perhaps sorted by month of conference (or better, month of deadline). Google will help find the current edition.

+1 for creating a calendar list sorted by month of deadline

You can also try callforpaper.org
it will provide all upcoming events(journals, conference, seminars, workshop, sessions). subscribe to its rss feed with particular keyword. and you can also post new academic events.

That link doesn't seem to provide the information mentioned in this answer.

I find it helpful to keep a spreadsheet of all the relevant conferences, with columns for the next submission deadline, conference URL, organisation, and organisation URL.
When I find out about a conference too late to submit, I still add it to my spreadsheet. I try to find out if the conference is annual, every two years, or what. I put down a rough guess for the next submission deadline based on the current deadline. That way I'm prepared for the following year.
Also, when I read a paper in my field, I always note where it was published (because the journal or conference might be suitable for my own work). If it's a conference, I add it to my spreadsheet with as much info as I can find.
This is in addition to looking for appropriate mailing lists, as the other answers have covered.


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What are factors leading to rising tuition costs over time?
Is there any published work that quantifies the roles of different factors on rising tuition in the U.S. over the past half-century?
I've heard a number of explanations bandied about, such as:

increases in admin overhead
IT infrastructure costs
Baumol's cost disease
more expensive facilities
reductions in state funding over time (public institutions)

What I'm looking for is some quantitative analysis that tries to estimate how much each of these different factors contributes to the average increases in tuition over time.

According to Les Perelman's essay that fooled an automated grading system (http://www.documentcloud.org/documents/346138-essay-awarded-a-top-grade-by-e-rater.html), high college costs are the result of excessive pay for teaching assistants.  :-)

@anon - Very nice. Don't forget the "private jets and trips to the south seas". (For those unfamiliar with the above, see this NPR article.)

The Delta Cost Project, a nonprofit organization in Washington DC, issues reports each year with information about college spending. The highlights of the 2011 report, which I recommend browsing through, states that:

For the majority of institutions, increases in tuition do not translate into increases in spending. In fact, at most public institutions, tuition increases attempt to compensate for lost revenues from state and local budget reductions, but actual tuition increases are less than half of the actual reduction in state and local appropriations.

Later in the report, other sources of tuition increases are listed, including increases in benefit spending for employees (primarily public institutions). Salary fluctuations are not significant factors; in fact, spending on salaries has gone down slightly over the past few years.
For those interested, I strongly recommend checking out the highlights listed above, as well as the full report, for more details.