When should I write a thank you letter to the author of a scholarly paper? If I read a scholarly paper and find it interesting and beneficial, should I write a short thank you letter to the author? Should I send the thank you letter from a .edu email address?

It certainly wouldn't hurt, and as a published author myself, I would say it would be very nice feedback, particularly if you include details about:

specifically any particular points/methods you found useful.
A brief outline of how you are extending the work.
Perhaps any question you have about the article.

This could be a good way to make yourself known in Academia, especially if the author is an influential scholar in your field.  However, a caveat, don't overdo it - in terms of being 'over the top' complementary or too many 'rapid fire' letters/emails.

But, it would more than likely be appreciated as it would be a validation of the author's work.


Should I postpone my MEXT scholarship application process until 2021 due coronavirus outbreak? The next month I plan to apply for MEXT scholarship for a PhD study. My study proposal is almost ready and I have my thesis already written in English. But due coronavirus outbreak I was thinking to do anything I can to be prepared and on the next year actually apply for.

The main reason is because I plan to wait for a vaccine first for coronavirus, because my N5 level of Japanese may not be enough to communicate with a doctor in order to receive a vaccine. Though I was successfully examined and received a JPLT N5 Certification.

Do you think that is a good plan?

At this point there are no guarantees. Things could be fine in a year or not. There could be a vaccine or not. Japan could be doing well or not. The pool of applicants could be stronger then or not. Travel may be easier or not. There are just too many variables.

Under the circumstances you are probably best advised to continue on with an application until you reach a firm decision point (acceptance, say). Perhaps more will be known then. But expect chaos in the near term. Too many governments are behaving incompetently and making bad decisions. That could change or not.


Should I tell students that it's my first time teaching the course? I'm a TA teaching a class this fall for the first time.  I've taught before, but never this class, and never felt an obligation to tell my students it's my first time teaching a given class.  But, being a bit more experienced I thought it might be a good idea this time by perhaps endearing me to my students, being so candid on the first day.  Does anyone have similar thoughts on approaching a first-time teaching role?

Recommend not on the first day.

I'm actually in exactly this situation for the fall term, so I was prepping myself mentally for just this issue. In my experience, expressing any uncertainty about the course on the first day prompts almost instantaneous pleading/negotiation/argumentation over any and all stated procedures (parameters for assignments, grading, due dates, etc., etc.)

Now, this is partly influenced by the fact that I work at an urban community college where the student maturity level can be quite low for certain courses. If you work at a more high-powered institution then the environment might be different. But I still think it best to be authoritative at the start, gauge the environment on subsequent days, and then if you feel comfortable admitting the situation and/or asking for feedback later on, you'll be more confident about doing so.


How to proceed after reject & resubmit I recently got a reject & resubmit which usually would not bother me too much, however, this case is a bit special:
The specific journal runs a single-blind peer review process. One review was very positive and the other one was extremely negative (if not to say rude). The AE and SE also provided their own comments and decided "reject with merit". Which is ok, however, there is scant evidence that the negative review has been done by my former phd supervisor. As indicated by the rude review we did not separate after my graduation in a good way.
The problem is: I do not know how to proceed from this point. How do i make sure that i will get a fair and (more important) ethical review process after re-submission? I'm also not sure how common it is to ask the authors for a decision about the resubmission (incl. a concrete time horizon) after rejection (note it is a top trier journal).
According to the peer-review process i should have no idea about the reviewers. However, it is not always too difficult to figure out (in particular if the particular research area is small and you have worked for years for a specific memeber).
Many thanks in advance!

Let me suggest two things. First is that you ignore the rudeness and take what is in the reviews you got to improve the paper as best you can. In other words, standard practice.
But, when you resubmit, let the editor know that you have conflicts, beyond the paper, with individual A (by name) and that you don't believe they can give you a fair reading. Ask that the editor not assign them as your reviewer. I suspect that this is an unusual request (in some fields), but that it would be honored. The editor needs honest appraisals, unclouded by personal issues.


Keeping track of all you have to do in academia Back when I was in graduate school and as a post-doc, life was fairly blissful. Only one big responsibility: research. Now as a faculty member I find so many things to do. Teach, supervise undergrads and grads, publish papers, perform research, participate in service/administrative activities, get funding, etc. Plus throw in family life, friends, etc.

I've looked at all sorts of productivity systems over the years (GTD, 7 Habits, etc.), and have settled on a simple todo list method, where I have a master list of tasks in a todo list  that I periodically review. The problem is the list just seems to get bigger and bigger. More gets on  the list than comes off, especially during busy seasons, like when teaching or when grants are due.

I realize that busy is part of the game, but how do you keep track of everything and not go crazy?

Another nice todo list system is Trello which lets you do things like add mini-check lists to items, make separate lists for each thing, add notes to items, add pictures to items, and add other people to items.  The ability to add sub-items helps a lot in that it makes it feel like I'm getting somewhere on large projects that take a lot of time and hang around in my to-do list for weeks.

Trello is also really nice for sharing/collaborating/delegating work.  In our lab, we have a Trello board for any projects where multiple people are collaborating so everyone is able to keep track of who's responsible for what.

Last, it lets you move your items around so that you can prioritize them.  Stuff that you need to get done sooner goes on the top while less critical stuff is on the bottom.  I also have a bit of a garbage cleaning policy where if it's been sitting in the low priority for a while and I still haven't gotten around to it, it goes into a theoretical "someday when I have free time" list.


Why have lectures in the information age? The primary method of instruction at most colleges is lecturing, where the professor delivers and explains a set of well-established knowledge to the students.

However, there are drawbacks to this: people have different goals, intellectual orientations, and levels of prior knowledge. What's more, the information delivered in these lectures is well established, well documented, and easily available online -- and for far less money than the average college tuition.

Can lectures be more effective than, say, reading a book oneself? I am unconvinced. Instead, I see people learning by imitation, reading, discussion, and practice. If education is a way to prepare for life outside of academia, shouldn't the method of instruction also reflect the ways people learn outside of that environment?

What advantages (if any) does lecturing have, that make it worthwhile in an age where there are so many other options? Is there any systematic, empirical evidence that supports the widespread use of lecturing?

Inertia/tradition accounts for many things. "Doing things they way they've always been done" [sic] is usually considered defensible, too. Also, people have already-existing mental models for what a lecture should be like, often including specifics about the subject matter.

The fact that information is available on-line is not wildly different from the fact that information was available in universities' libraries. Yes, a sufficiently motivated person can simply go to the internet/library and find lots of information. A potential problem is that there is too much information, that it is fundamentally chaotic (despite our attempts to impose order or develop "search engines"), and fundamentally hard for a non-expert to evaluate. Even worse, a non-expert may fail to realize that they are failing to correctly evaluate information. :)

Still, yes, very many classes/lectures are boring, and attendance is often easily replaced by reading the designated textbook or other sources. However, in several decades of observation, many students (at all levels) either prefer or have become accustomed to a kind of passivity, so that they'd rather show up somewhere at a regularly scheduled time, see their fellow students, and have the pace and content dictated to them by even a fairly boring lecturer.

In my own student days, I did not like going to classes, for the obvious sorts of reasons: for one thing, if one had read the book, a slo-mo flawed, re-recital of it seems pointless in comparison to just re-reading at one's own speed. Second, if one found the material interesting, why stop? Why not read ahead? Why not look at other sources, too, for complementary viewpoints? Why not look at related stuff? (This was as feasible in libraries as it is on the internet, with perhaps two added advantages: there really was not much junk in libraries, since it was filtered, and, second, the chances of serendipitous discoveries in libraries was larger than on the internet.) Such a process inevitably makes the "canned" lectures seem crazily irrelevant.

(Also, years ago, libraries were some of the few reliably air-conditioned places!)

But let's ignore the problem of student passivity, and ask why/how a lecture _could_be_ better than just reading a book or searching on the internet. Arguably, a lecture is not better if it just amounts to reading from the book, copying from it onto a blackboard, etc. I would claim that trying to make lectures simply present text-book material is a big mis-use of the medium! That is, systematic presentation of all the details belongs in a book or on-line, but not in a lecture. Oppositely, what could be in a lecture that could not be in a book or notes? "Affect", meaning intonation, gestures, facial expressions, theatrical effects, and so on, are hard to put into writing, but (by "lecturers" capable of it) can be put into a lecture. This includes reaction to facial expressions and body language of the audience/students, and conversational interaction if the group isn't too large. For example, lectures can include "pep talks" that would be hard to fit into writing. "Reassurance" can be done live better than in writing, I think.

Another feature is the "live/real-time" aspect: a lecturer (in mathematics, my field, for example) can literally do things in the lecture room, live, in real time, with voice-over narrative, in effect. That is, the audience can witness the genuine activity as exercised by an expert practitioner, with accompanying critical and methodological comments. Yes, up to a point, textbooks and monographs could be written in such a fashion, but it seems that stylistic pressures move them in the opposite direction, aiming for a sort of artificial perfection that can only be achieved by much editing! Too often it seems that writing aims to create impressive edifices rather than be accessible, helpful ... and a live lecturer can easily do better, if they try.

So, for my own lecturing, I definitely do think in terms of "adding value" beyond what students could derive from written sources, and in terms of using the medium in ways that distinguish it from static written sources (and not having a lecture be a bad re-copying of those written sources).


How to publish a corrected proof for a claimed mathematical result? I work in the field of theoretical computer science, and I have published a paper with several results. A few years later, a reader reported to us an error in the paper. The paper claims a theorem X, but the proof given actually shows a somewhat weaker result X'.
Thinking about it, I have been able to come up with a proof of the originally claimed result X, using somewhat different techniques. The new proof is not interesting to merit publication as a new paper, but the fix is not trivial either so I'm not fine with leaving the mistake as-is. Besides, result X is not central in the paper, and it is indeed correct (only the proof was not), so this is not a situation where we should think about retracting the original paper altogether.
I'd be interested in the community's opinion about what's the best way to proceed to publish this fix to an erroneous proof. I can see at least two options:

Option 1: publish a revised version of the paper with the original claim of X and the new proof (and a comment that the original version of the paper had a mistake). I think this would be the most comfortable option for future readers. That said, it may create confusion as the original buggy version of the paper will still be around. Plus, I would imagine that ethically I cannot do this without approval from all authors of the original paper (at least one of which has now left academia).
Option 2: publish a separate note on arXiv containing just the new proof of X, and publish a revised version of the paper providing the proof of X' plus a pointer to the new note for the proof of X. This has the advantage of leaving the original material essentially intact, plus the note can be authored only by the people who are still involved. But it is less pleasant to the reader (who must jump to ta different document), and it is more work for us (since one would need to re-explain the whole context in the note, etc.), all for a not-so-interesting fix.

[With both options, I would publish the updated version of the paper simply on arXiv -- dealing with the publisher would only complicate things I think.]
What do you think would be the best option? Essentially the question can be summed up as: when is it better to fix errors in a paper simply by updating it, and when is it better to publish the fix as a separate note?

I had a similar problem with one of my conference papers. We posted a revised version on arxiv, specifying in a footnote what the mistake was and how it was corrected. The correct proof made it official appearance in a journal paper that was partially based on the the conference one.


What is the meaning of "person specification" in a job advert? I am going to submit my application to a postdoc in math. In support of my application, I have been asked about what I can do, and they have mentioned that

You should pay particular attention to the person specification as you will only be shortlisted if you can demonstrate that you meet all of the essential criteria.

But I do not know exactly what they mean by the above mentioned statement? Can I provide a brief description of my scientific background and its relation to the advertised project?
There exists a brief description of the project, including the area of research.

I've seen this terminology particularly in the UK, though I don't know how widespread it is. In each of the UK jobs I've seen with this phrasing, the "person specification" was a very clearly labelled part of the advertisement for the opening, or in some cases a separate PDF document. It contained a bulleted list of items clarifying both "essential" and "desirable" qualifications for the position.
I think your contact is urging you to consult such a list. If you have not gotten your hands on this kind of document regarding the position, look carefully for it where the job was advertised. If you still can't find it, I would write back and ask for a copy or where you can find one.
If part of your written materials for the application includes a personal statement, that statement should briefly highlight specific aspects of your background which demonstrate that you fulfill the listed items. Frankly I'd reference the specific items on the list.
I have not personally done job recruiting, but it is my impression a literal checklist of whether these items appear in your application will be made.


Use of Wikipedia images I created myself I have created several images for Wikipedia and would like to use them for my own poster/talks as well. However I am concerned that my colleagues will assume that I took them from Wikipedia and will consider it bad practice to use images from Wikipedia instead of my own and secondly to not reference them. How would you clarify that?

I think the problem here is that you (a) don't feel like you should be citing the source of this, since you made it yourself but (b) think this will be viewed as plagiarism from Wiki (or, at least, laziness). It seems to me the best way to resolve this is to cite your source, and cite it as yourself via Wikipedia. A short note like (Wikipedia, Original Artist Jane Doe) makes it clear that yes, this is the image from the Wiki page but also that you made it.


Copyright on a research photography I was part of a research group in a research institute I called 'X'. In this research we used a very interesting, colorful technique so I take some pictures for myself that are very artistic. Now I want to present them in a Scientific Photography contest organized by the same institute 'X'. I signed a confidentiality agreement with the institution and my research advisor. The thing is I need an author's written authorization for reproduction of the images in order to participate in this contest. At first I thought I was the author since I was the one who took the photo, but seems that in the agreement I signed says that all products of this investigation are property of the institute 'X' and I don't know if this has something to do but the camera was also property of the lab. So, who should I ask for the authors written authorization? Or I don't have to ask for it at all?

Ask the head of the research group that you were part of.


Cover Letter for PhD Application I have to write a cover letter for a PhD application (in theoretical physics).

I didn't find any useful sample about this. Does anyone have any suggestion?

Moreover, I have to write a research statement. I don't know how I can write them in different ways.

Several different templates are available on the net, it depends only on your taste!
I would like only one thing: write it in LaTeX. If you are not familiar with LaTeX or you don't feel comfortable with it, Theoretical Physics is not for you. Obviously I'm joking, but not completely...
Anyway, without too much efforts, on the net I found in particular this template that is really suitable for many purposes (actually, with some modifications, is the one I use for my letters):

As you can see this is very sober but direct and clear.
If otherwise you fell very comfortable with typing in TeX, I suggest you to try to emulate some template in LibreOffice downloadable on the net. In particular I recommend this one, in particular the one at page 23, but many others are really nice.
Therefore, I would like to quote also this answer from SE Academia that partially answer your question. In particular I stress the importance of these sentences:

What is unavoidable to write
Make your cover letter personal, remarkable (i.e., stands out from other cover letters), specific to you and specific to the position at hand. Be enthusiastic. Be specific. Show that you've put thought into the position and why you are applying.
Relate your specific skill sets and previous experience to the programme you are applying for. Relate the content of specific aspects of your CV to the programme:
"During my masters, I enjoyed working on the topic of A, which relates to your programme [in this way]"
"I worked three summers at company B, where I gained experience in topic C ..."
"I visited your university in March last year and was impressed by ..."
"I read paper entitled 'D' published by your group at 'E' and was interested in ..."
"I recently published a paper 'F', which I believe compliments work by 'G' in your department on 'H' ..."

Good luck for your application!


Going to Industry and Keeping Publishing I'm currently a postdoc in theoretical computer science. My position will last for about 9 months. I have a good track of publications and enjoy a lot working at academia, in particular I enjoy to solve problems and write papers in my field. But I think that it would take something like 2 to 3 years to get competitive for a lector/tenure track job.

The thing is that I'm married with children, and my wife has a permanent job. So she will not be able to travel with me if I need to do another postdoc elsewhere. Therefore, I'm considering applying for industry jobs. I do believe that some types of jobs in within the industry would also be very enjoyable. But my goal would be to keep publishing and then eventually get back to academia when my CV is competitive enough.

My only problem is: Once I go to the industry, how to keep publishing? I mean I am pretty independent and good at writing papers alone or in collaborating via internet. And I'm also used to write papers in my spare time, during the night and on weekends. So I'm not worried about the time to keep doing research. But I'm afraid that without an academic affiliation, the probability that my papers would be considered for publication in conferences and journals would decrease.

Suppose I work in some enterprise in the automotive industry, or telecommunications industry, or even as a consultant.

Question 1) What affiliation should I put in my papers when submitting to conferences and journals? Should I put the name of the enterprise, even if the research is not being done there?

Question 2) Would an affiliation outside academia decrease the chances that my papers are accepted in theoretical computer science journals and conferences? Of course I know that some affiliations such as google, microsoft, etc do not harm, but I'm considering some jobs in much less well known companies.

Question 3) Is it possible to go back to academia after some years in industry if I keep my publication record high?

I am a good example of how it is quite possible to keep up a strong publication record in industry, as long as your job supports it. I submit my Google Scholar profile for evidence: I moved from postdoc to industry in 2008, and though I have contemplated (and been offered) opportunities to move back to academia, to date I have actively chosen to continue in my current position.

Likewise, no healthy scientific community will hold a prejudice against authors from industry, any more than they hold prejudice against authors from less well known universities.  Unhealthy communities do sometimes have cliques that make it difficult for anybody outside of a clique to publish.

In certain cases, you can even have an advantage in research when you come from industry, as it is often useful for academics to have "industry partners" who often have a broader perspective are capable of doing things that they are not.

You do, however, need to have a job that supports publication.  For that, I recommend looking into research consulting companies, rather than normal "product" companies, where you will typically have little time to publish.  If publication can be part of your job, you can keep up publication; if it is a "second job," it will be far harder.


Find a specific paper on information retrieval method supporting literature research searching not by keywords but by documents About 2012, I did a literature research on the following topic but unfortunately lost my results. Specifically one paper comes repeatedly to my mind, therefore maybe someone knows about this or subsequent research.

The research question of that paper was about information retrieval, specifically full text mining of scientific literature to automate literature research.

The researchers built a custom spider/search engine which takes as input not a set of keywords but set of documents.

They described that this approach allowed them to find relevant branches of research they were not aware of.

Which paper was it and/or what is state of the art regarding this topic?

This is probably not the older article that you are looking for, but a colleague of mine published an article that shows how to identify the most relevant literature using free biblilometric tools such as VOSviewer. That is, by beginning with a topic search on a citation database (e.g. Scopus or Web of Science), you can identify the most relevant body of literature based on cocitations and other bibliometrics:

  Walsh, I., & Renaud, A. (2017). Reviewing the literature in the IS field: Two bibliometric techniques to guide readings and help the interpretation of the literature. Systèmes d’Information et Management. Retrieved from https://www.researchgate.net/publication/316560668_Reviewing_the_literature_in_the_IS_field_Two_bibliometric_techniques_to_guide_readings_and_help_the_interpretation_of_the_literature

Perhaps you'll get lucky and the original article you're looking for might be in their reference list.


How long does one need to keep the original data of a study / publication? Most journals require to make data available at the time of publication (repository / upon request or similar). But for how long does the data need to be kept (field of on (bio)medicine)? This would especially be interesting in relation to the scientific wish to keep the data forever vs the General Data Protection Regulation (GDPR).

Journal guidelines as below seem not to specify this ...

https://www.nature.com/nature-research/editorial-policies/reporting-standards
https://authors.bmj.com/policies/data-sharing/

This is a question you should ask the funding agency that is paying for your work. They usually have requirements for how the data that is produced should be handled.

As an example, this is what the main German funding agency DFG says:

  Den Regeln der Guten Wissenschaftlichen Praxis folgend sollen Forschungsdaten in der eigenen Einrichtung oder in einer fachlich einschlägigen, überregionalen Infrastruktur für mindestens 10 Jahre archiviert werden.

My rough translation:

  Following the rules of good scientific practice research data should be archived in your own facility or in a topically relevant national infrastructure for at least 10 years.

There are certainly different considerations when the research data contains private information, e.g. patient data. I can't say anything about the regulations there, I'm only considering public research data that doesn't have any privacy implications.

In general the scientific community benefits if the data remains available forever. And while the 10 years in my example are a minimum, many parts of the produced data like the publications and depositions of structured data into repositories like crystal structures to the PDB remain archived indefinitely. And many repositories like the PDB are steadily increasing the amount of raw data they would like to get along with the final output.


Selecting license for personal professional site's content It seems that creating personal professional websites by aspiring and experienced researchers is a mainstream trend today (that includes full-featured sites as well as blogs). Based on multiple recommendations from people's answers and comments on this site as well as my own opinion on the subject, I have decided to jump the bandwagon and create my own full-featured personal professional site. I still plan to maintain my profiles/pages on various professional/social sites, such as LinkedIn, ResearchGate, Academia.edu, about.me and some others. However, I envision the planned site as a centerpiece of my personal professional branding strategy due to higher independence (no platform lock-in), much more flexibility in creating, managing and styling content, thus, providing much better opportunities to express thoughts, which is essential to any scholar.

Working on my website, I included slightly customized versions of free templates of Privacy Policy and Terms of Use. The latter document contains references to software licensing, but does not address the licensing of the website's contents and users' contributions, which I think is important.

In this context, I am curious about pros and cons of selecting particular content license, including the Creative Commons license. When answering this question, please keep in mind that, while significant part of the website's context will be related to academia and research, some planned materials will (might) be of dual nature, that is, focused on either academia or consulting, or both.

For licensing personal content, you almost certainly want to either use one of the Creative Commons licenses or else declare your content All Rights Reserved.  There is actually not one, but seven Creative Commons licenses, which span a wide range of preferred usages (here is a handy tool for choosing a license to use), and the licenses are  well-maintained and highly compatible with themselves and others, even internationally and in complex remixes.

In general, then, if you want your content to be shareable, you should choose a Creative Commons license, and if you want it to not be shareable, your should declare it All Rights Reserved.  Alternate licenses for shareable contents are generally not as compatible, well-maintained, or well-understood by others as the Creative Commons family, and thus will generally be no better (and often worse) for sharing.  Alternate licenses for non-sharable content are generally intended to support particular commercialization relationships, and would be negotiated when such a relationship is being established.

Of this set of options, for a personal website, I would generally recommend CC-BY.  This is the most lightweight and flexible sharing arrangement, and thus generally allows the most potential for increased personal visibility (attribution is always required).  If you're planning to put up major works that you think others will want to publish commercially, then you might want to consider using All Rights Reserved for those works, but probably not for small works or for the web pages that contain them: at an early stage of your career, attention and credibility will be much more valuable than the largely non-existent possibility of some sort of royalties.


Is expanding the research of a group into machine learning as a PhD student risky? I have the opportunity of doing a PhD under the supervision of an expert in medical imaging at a top institution. Currently their group does not conduct research into the application of machine learning to medical image acquisition and processing. The purpose of the PhD studentship would be to pursue research into this. The department has significant machine learning and signal processing research groups whose seminars I will be able to attend and academics I can have contact with.

The supervisor has not for some time (before deep learning) pursued research in machine learning. The PhD itself is as yet not strongly structured and will initially require a deal of exploration and prospecting before its final form is decided.

Given that there is a safe fallback of medical imaging I do not foresee a risk to completing the PhD. However, as the only member of the group pursuing machine learning would this be a very risky PhD to embark on, particularly considering that afterwards I intend to pursue a career in academia? Are there any benefits?

I would ask about having a co-supervisor. Having access to esteemed DL researchers is great -- but they will have limited time/interest in helping you if you are not "formally" their student. If you manage to find someone in this role, I think your position is just about perfect.

If you don't manage to find someone in this role, I have three main concerns:

You will spend a ton of time re-inventing the wheel. For example, can you train a CNN on ImageNet from scratch? There are a lot of caveats needed to obtain state-of-the-art results (e.g., dataset augmentation, regularization loss, etc.), and you will likely rediscover them one-by-one (or, use a black-box model you don't really understand). A DL expert would likely already have working code and could explain it to you, allowing you to jump right to the research. (Yes, there are open source codes...but in my experience, they all require a lot of work to be both transparent and accurate.
Mathematical rigor. It's easy to just learn ML/DL at a "technician level" -- but as a PhD in it, you should really understand it a mathematical level if not a theorem/proof level. It can be difficult to do this on your own.
Problem selection. Your medical advisor will likely find it super novel to run existing techniques on medical images. There may even be a novel application here, on the medical side -- but on the ML side, this is not really interesting, it's just a straightforward application of one technique to a straightforward problem. This is maybe OK if your interest is entirely on the medical side -- but if you want to do something also interesting on the ML side, you would essentially be on your own to come up with something. That will be difficult to do (for the first time) without advisors on both sides.

Those are the main blind alleys I see. Of course, there is also a ton of upside -- this sounds like a very interesting, prestigious position that would position you well for an academic career. Only you can judge this tradeoff.


How to include experiments vs state-of-the-art papers with no code I am working a paper which offers an algorithmic improvement, which is measured in both the quality of the results, and the time it took to achieve them.

There are 3 recent (relatively) papers which deal with the exact same problem. One of them i am building upon, and my improvement (while can be used in other fields as well) is geared for it. The improvement is significant, and I have all the required tools in order to reproduce its exact results and prove it.

However, the 2 other Papers, which both (claim) to be better than the first, lack the required code in order to reproduce the results.
I have tried contacting the authors, in more then one way, but no reply.

Also, according to paper #3 (which is the most recent one), paper #1 actually performs better than paper #2, A thing which contradicts paper #2.

I have an implementation of paper #2 (Not my own, or the original) which exhibits very poor results.

I am not sure how I can move on from here - Doing my own implementations for #2 and #3 is both very time consuming, and I could easily have a bug or two. And a reviewer can claim it was biased against them.

And obviously, If I wont benchmark against them, I could not claim to be The state-of-the-art solution for the problem (even if the improvement I show vs #paper 1 is bigger than they does).

Any advise would be great!

In this situation we always just say "we attempted to compare our result against XYX et al, but could not access a working implementation."

If a reviewer were to complain, we might say (to the reviewer, not in the paper) "in what way does #3 move the field forward if it cannot be used by anyone".


Citing references consistently Many of the journal references in the bibliography of my thesis contain bird names. Journals use birds names in the titles of papers in at least four different ways:

Titlecase, eg Teal
Titlecase plus scientific name, eg Teal Anas crecca
Lowercase, eg teal
Lowercase plus scientific name, eg teal Anas crecca

These different ways of using bird names makes my bibliography look untidy and inconsistent.

Should I adjust the titles of the papers in my bibliography so all bird names are used in a consistent way? Or should I use paper titles exactly as how they are given?

As a general academic principle you should not adjust the titles -- or other essential bibliographic data*, e.g. the form and ordering of the authors' names -- of papers that you reference in any way, with the possible exception of necessary typographical concessions for "exotic" characters.

(For instance, in my branch of mathematics is it common to use the cyrillic letter Sha for something named after a Russian mathematician whose name begins with this character.  If you simply don't have cyrllic characters available, you have to do something else.  But even in this case it would be better to try to take a little trouble to "get cyrillic characters".)

So my answer to your question is no: it is obviously not your fault that different papers you cite refer to teals in different ways.  So if there is any untidiness and/or inconsistency, you are simply faithfully replicating it, as you are obliged to do.

This answer comes from someone with precisely zero avian-specific academic knowledge.  So it couldn't hurt to get a second opinion from someone in your field.

*: I confess that I sometimes mess with "inessential" bibliographic data.  For instance, most journals come with a volume number followed by a number of the issue within that volume, and I usually omit the second number: you simply don't need it to access the paper.  I don't specifically endorse this practice and mention it only for "professional honesty", but in my defense I just checked around and I am far from the only one who does this.

Moreover in some fields there are different formats for referencing.  In my field (mathematics), on the one hand we are not too picky about the format, and on the other hand we have standard repositories of all papers: MathReviews/MathSciNet and Zentralblatt, from which I assume that most contemporary authors simply copy the bibliographic data (and then the philistines among us delete the number of the journal within the volume).  It is a good idea to choose a consistent format throughout all your bibliographic references: e.g. put last names first always or never, and so forth.  But still: the title is not yours to monkey with, as far as I know.


Permission for using publicly available questionnaires in Dissertations I have used and/or adapted several questionnaires for my dissertation study. I have already asked the authors for permission to use their scales. However, I have not received a reply from an author about using his scale.

I wonder if we have to have the permission of the authors when we use their surveys (when the questionnaire items are published and publicly available), or is it a courtesy to ask for the permission. Is it still okay to use a public scale when no confirmation is received from the author who developed the scale?

Thanks for any suggestions!

Cite them.

If the questionnaires are published then you do not need to ask for permission, just give them credit.

In Psychology there are some very popular questionnaires that were presented in papers that have been cited more than 5000 times. It would be a full-time job to reply to every person's email who wants to use it!


Should postdocs give fewer (or otherwise different) status updates than PhD students? This question is a bit weird to ask because generally speaking, a normal answer will be "the same way you used to work as a PhD student" but I am not sure if I picked a "bad" habit from my previous experience.
Context:
As a first task as a postdoc, I have received a short abstract with an expected research outcome (a detailed technical report) and some sub steps to achieve the research outcome. These sub-steps are important tasks on their own and will need some research and time, I understand that. So, here is what I did, I read articles in the first week and I prepared a small draft (one page) highlighting key ideas that will help me achieve the first sub-task. The issue, is that I needed some further clarification about the abstract as this will help me decide which direction I should follow next, but at the same time, I wanted to send something to the PI in the first week and not "disappear" after receiving the research abstract, but I haven't received a response in 3 days and I don't know if I created a good impression.
Now I am wondering, how does a postdoc work in the first place (research methodology)? am I expected to have big results every-time I reach out to the PI? When I was a phd student, I used to send weekly (sometimes 2 weeks) updates to my supervisors. These updates were either progress status or problems I was stuck at! Is this approach acceptable for a postdoc?

I'd wager that both 1) the variance in expectations among PIs and 2) the variance in communication styles among graduate students or post docs far exceed the average distinctions between grad students and post docs.
Many labs will have regular group meetings, perhaps weekly. One would expect both grad students and post docs to attend and give regular updates at these meetings. This was my own experience. In some fields, both grad students and post docs may need more "every day" training in the beginning to get up to speed, which might mean more frequent check-ins during that time.
Other labs, and in fields where work is more independent, grad students may mainly check in when they have either produced something worth sharing or are stuck. Perhaps in this context, post docs will check in less often if they have gotten better at solving their own issues. Alternatively, professors may be more proactive in checking in with their graduate students to make sure they aren't wandering off into the woods.
I'd recommend anyone starting in a new position (graduate student, post doc, or employee of any sort; within or outside of academia) have an early conversation with their supervisor to compare expectations and preferences about communication, including frequency (ideally, this would occur in some form before even taking a position, but it's good to revisit once starting, too). This sort of direct conversation is going to be a lot more productive than trying to divinate expectations from the latency or content of email responses, norms experienced by others in other positions, or ones own past experiences. You can start the conversation with how you've interacted with supervisors in the past, if you'd like, and share how you thought that worked well or didn't work for you. Your supervisor may have other ideas. I'd suggest finding a working compromise between the two.


Is it okay to submit a paper from a master's thesis without informing the advisor? I would like to submit a part of my master's thesis which is more or less close to an end. I wrote the entire thesis without having much feedback from my advisor as he's in a different city and we had literally no chance to meet except a few times. The feedback he had provided was too little and I want to submit a part of the thesis to a conference on my own. I will give his name of course while submitting but do I have to also inform him?
If I have to, then he might not approve this as he contributed very little and still he doesn't like my research much.
What should I do according to your experiences?

Should I inform him and bare his negative comments about not submitting at all?
Or should I submit as single-author paper as I, from the beginning to the end, was only not the writer (of course it's my thesis) but also the solely contributor to this thesis? (He even said it to me as " you did very much well in fact, on your own", in one of our meeting.)

edit: by giving his name, I mean not as a formal authorship, rather than as a footnote, sth like that.

Under no circumstances can it be ok to submit with his name on it but without his explicit consent. This wouldnt be ok if he'd be enthusiastic about your research, and if he is not particularly fond of it, this will quite certainly end badly.

If you are confident that your advisor did not contribute to the planned submission in a meaningful way, the default course of action should be to sent him a message informing him of the planned submission and thanking him for the guidance received. That way, if he disagrees on not having contributed, there is a chance to fix stuff before they blow.


Is it ethical to get suggestions/corrections about my PhD work from a consultant? I am doing a PhD in Mechanical Engineering. I have little experience with CAD programs, and I have to design an assembly in my project for manufacturing. As my supervisor is busy, and also not a specialist in CAD, I am thinking in hiring a CAD consultant of a company. Her tasks are basically to verify my CAD parts and ensure that everything is fine for manufacturing, and, if it is not, to send correction and comments about what to do to fix the parts/assembly and brief tutorial on how to do it.

My question is: if I do the work myself and only get suggestions/corrections from someone else, can I encounter any problems later, like having my PhD degree revoked?? I don't want to ask help from my supervisor, as I don't want him to spend 20 hours or more with my work.

Please tell me if I can do it; and if yes, if I need to inform someone, or put something on the thesis regarding it, or anything else.

You need to do two things here:

You should ask your advisor in advance whether this is acceptable.  The answer may depend on the details of your situation (exactly what is involved in this CAD verification and how central it is to your research), and your advisor is one of the few people who can give you a definitive answer.  I'd bet that it will be OK as long as you do the design yourself, but my opinion is not so relevant: if you end up in a disagreement with your advisor, it won't help if you complain that people on the internet assured you it would be OK.
You must acknowledge this assistance in your dissertation and papers, the same as any other contribution to the work.  This is a matter of intellectual honesty.  However, acknowledging the assistance afterwards can't substitute for asking your advisor in advance.  (In particular, your advisor might say "There's no issue of honesty, since you described exactly what you did.  However, you hired someone to complete a substantial part of your thesis, so you have not done enough yourself to graduate.")


What is the weight on the applicant's personality for tenure? Assume that someone is an excellent researcher (many awards and at least 7-8 publications a year) and a very good teacher but he is not "liked" by some of the tenured faculty in the department (due to differences in opinions on how things should go or how decisions should be taken regarding different matters in the department).

Shouldn't being an excellent researcher and a very good teacher outweigh any social issues?

This is a really contentious issue (typically referred to as "collegiality" in the context of tenure decisions), and there's no clear standard for what to do.  There have been a lot of opinions, such as this one from the American Association of University Professors, but there is no universal rule.

On the one hand, it's outrageous to deny someone tenure just because you personally dislike or disagree with them.  That's an abuse of the tenure process.  The goal is to end up with a good colleague, not a friend or sycophant, and other considerations are not relevant.  Furthermore, there's a danger of discrimination if the current faculty prefer to be around people like them, which just compounds the individual unfairness.

On the other hand, how someone acts can be a fine reason to deny tenure, regardless of how good their research and teaching are.  For example, it would be a mistake to tenure an abusive jerk.  Being a good colleague involves treating people decently and participating successfully in committees or other administrative tasks.  If you behave poorly enough that you can't do that, then you shouldn't be a member of the department.

Of course the difficulty lies in distinguishing between these possibilities.  What one person sees as courageously standing up for their beliefs in the face of opposition, others can see as being rude and disruptive.  It can be difficult to tell whether someone is behaving in a genuinely objectionable way or you just don't like them.

I'd recommend extreme caution in these sorts of cases, since there's great potential for unfairness and poor decisions.  (When these issues come up, it's a good time to think about implicit bias.  Maybe this behavior wouldn't have bothered you if it had come from someone else?)  At the same time I can't endorse a policy that says it doesn't matter how you treat your colleagues, so the best I can say is "it depends."


Difficult adviser and personal improvements: How do I move forward? I am a second year clinical psychology PhD student. I have had some difficulties with my adviser in terms of never feeling good enough or that my efforts are acknowledged. The adviser has recently made more explicit comments regarding the lack of progress I have made on my critical/academic writing skills. As background, I came straight from my undergraduate psychology program (with a BS) into this PhD program. All the other members of my cohort have had 2+ years of research and this type of writing experience. So from the start I have felt that I have had to make up for my deficit. However, I'm not making the improvements that my adviser wants to see. The most recent discussion with my adviser ended with telling me that I am causing serious concern about my ability to complete the program and that maybe a less writing focused career would be better. Needless to say- I lost it. I have no plan b, and this is my dream. I have clinical and research plans that I am very passionate about but I do recognize that I am in the "needs to improve" category in terms of my academic writing ability. So it's this balance of seeing I do need to improve, which is virtually why we enter grad school. I have only had the last year and one month (I began my program in Sept of 2014) to begin developing and working with this academic writing style.

The first of my two questions is, has anyone else experienced such words of discouragement from an adviser? I don't know how to un-feel or un-hear those words that felt like a punch to my stomach.

Secondly, have any other psychology (or any discipline) students experienced difficulties in academic writing? If so, how you did you improve or what helped you make the necessary strides to improve at a faster rate? I have bought various writing books, I have writing meetings with my lab, and what seems to be the best advice from friends in the field and the books-- practice.

I want to improve and exceed. I just feel so discouraged when the person who is meant to mentor me has virtually given no helpful feedback on how I can improve, because the response to my inquiry on how to improve was I don't know and I feel so discouraged.

Thank you to all who read this. Everyone have a great day!

First of all, even good writers find academic writing somewhat difficult to learn. But it can be learned. Judging from your post, you can write coherently, and don't struggle with spelling or grammar. So I don't think it would be that difficult to learn the skill.

I'd like to recommend a book. It's entertaining, and gives really good insight into what makes academic writing different from other forms of writing. I think you will find it very helpful.

Here's the book: Scientific Writing 2.0: A Reader and Writer's Guide [ISBN: 978-981-4458-75-7 (ebook)]. If you buy it direct from the publisher, you can get it DRM-free, but you have to download each chapter separately. (On Linux, you can use pdfjoin to join the chapters into one big book.) Or you can buy it in one piece from other places, but with DRM.

Another thing I suggest is that when you read other people's academic writing, pay attention to how easy you find it to understand what the author is saying. When you find an article that is especially clear and easy to read, try to figure out what about the writing works. Likewise, when you find an article difficult to understand, identify the writing problems, and think about how the author could have made it better.

I'm a PhD student myself, and one thing I found helpful for my first few papers was to write a rough draft in an informal, conversational style, as if I were writing an email to my advisor. Then I would go back through the paper and make it a bit more formal. It's a lot easier to make clear writing more formal, than to make formal writing more clear!

Finally,  point to consider: when your advisor complained about your academic writing skills, are you sure that he or she was really talking about writing, as opposed to how you structure the article, or whether or not you incorporate suggestions, or even the methodology you used in your research? The reason that I ask is that, again based on your post, you appear to have reasonable ability for non-academic writing. Advisors can have students who are less than fluent in English, or have poor grammar. Getting that worked up because a student is struggling a bit to learn academic writing this early in the game seems a little surprising.


How to highlight language abilities in cover letter for a scientific research position? I'm applying for a scientific research position at a Welsh university and one of the desirable skills is to demonstrate an understanding of the bilingual nature of the University.

As I am fluent in Welsh, I would like to add a sentence to my cover letter stating that I am a bilingual. I would like to write something that makes them feel that it is important to have someone that can speak Welsh and that this would benefit the university.

Can anyone suggest an appropriate sentence to include?

To address your specific question, I would propose the following sentence for your letter (or something similar to your liking) to highlight your language skills. I would position it toward the bottom, in the concluding paragraph:

  I also believe that my fluency in Welsh will contribute to my ability
  to effectively support the university's bilingual nature.

(alternative wording):

  ...the university's mission of bilingual service.

I would not worry about providing any additional evidence of Welsh proficiency (as a letter written in the language) as you only want to submit the exact documents required in the application, nothing more. If there will be any need to ascertain your language ability, it can be easily done in a quick chat as part of your interview process or by phone.

Good luck!


PhD application research interest I am applying for PhD programs in the USA, one of the schools requested a PhD research interest. The problem is I do not know how to write it, and I didn't done any research in my masters degree, are there any solution?

For the abstract just state you did a masters without a thesis. Universities are used to the fact that not all applicant followed a standard model for their prior studies.
As for research interest I’m unclear what the challenge is? I would pick a topic that is not too general (cell biology) so that the interest is hard to elaborate on or too specific (Actin-related protein 2/3 complex subunit 1B) as to suggest hyper-specialization. Make sure you pick a topic that can be studied in the program you are applying to and explain why it is interesting to you.


Can I present my submitted work for publication as a poster in a symposium? I want to know that if the work presented as a poster in a symposium should be a work in progress or could it be a published work or submitted paper?
The field I am concerned with is biophysics.

I am not in biophysics - I'm in the health and social sciences, so this may be different for you. However, I would saw that it depends on the situation. Rirwt, some conferences have specific policies against presenting material that has been previously published. So, presenting a paper that has already been published may be frowned upon (thought I've been to many conferences with this policy and have seen presentations that have been previously published papers). The main concern is duplicate publication. So, if your conference fully-publishes the works that are presented (papers, posters), then publishing a finished product in both the conference proceedings and a journal article may be frowned upon by the conference.

Now, if you are presenting a work in progress and it will be different than a future or past published paper or presentation, that is usually acceptable. I have done this and have used the audience comments to help with revisions or with ideas for turning the paper into a second paper with a different focus.


can I not mention that I have will complete a PhD degree while applying for another one in another country I am a second-year Ph.D. student/ RA from a university in country A. I had no problem with my laboratory or supervisor; however, as I could not speak the country language and was not able to find a post-doc position due to COVID, I applied for another Ph.D. positions in the same field in an English speaking country (B) where I can immigrate and settle. In the application form for the universities and during my interviews I mentioned that I am a Research assistant, omitting the fact that I am a Ph.D. candidate. Also, my supervisors mentioned that I am RA in their recommendation letters understating the fact that I want to go to an English-speaking country. The problem is that due to my successful publications our department from country A decided to grant me the Ph.D. degree at the end of this year.
I read some posts that mentioned that omitting your academic records is the same as falsifying them. I am afraid if I go to country B without mentioning that I was in fact a Ph.D. candidate and RA and get in huge trouble, so what should I do?
Is it be unethical if I omit this fact that I would have a Ph.D., refer it to RA and start the second Ph.D. in the same field in country B, or should I contact the prospective professors from country B and tell him/her that I did a mistake in my application?

The comment of Jeff is worth considering. Do you really need a second doctorate to migrate.
But, under the circumstances, send a message to the new university stating that since your application, you were awarded a PhD, but, assuming you want to, that you still want to continue your application and enter the new program. Stress that the research proposal will be different if accepted.
Hiding the recent degree could come back to harm you.


Two years into my PhD program, and Mom is dying of cancer. Should I tell my advisor about it? I just finished my 2nd year of PhD, and my mom has been dying of cancer since the end of my 1st year. She nearly died in January but thankfully pulled through. She was just diagnosed again a few weeks ago and her prognosis is not good (resistant to chemo and can't get another surgery).

My cognitive abilities and general state of mind have suffered as a result of this situation. My research is very mathematical and being unable to stay focused for longer than 20 minutes really prevents me from making any progress. My emotional/mental state has also been seriously affected. I managed to pass my qual and aced my classes the past 6 months, but lately things are getting a lot worse.

I am hesitating if I should tell my advisor about my mom, but I feel that I'll just sound like I'm making excuses.

Quitting is NOT an option because I have never thought about it and I always wanted to do research since I was in high school.

My deepest sympathies for what you are going through.

You should certainly tell your advisor. No reasonable person would believe that you are using this situation as an "excuse" for poor performance.

Understanding your situation will help your advisor do his/her job: advising you according to your current needs and circumstances.

Your advisor may be able to direct you to mental health and other support services at your university that can help you through this time. He/she can also make you aware of other options that are available under exceptional circumstances: for example, a short leave of absence if you feel it is necessary, or an option to delay a comprehensive exam, or other similar concessions that can take some of the academic pressure off you while you focus on regaining your mental and emotional health.


"Withdrawn" grade from an undergraduate class vital to my Master's application I am applying for a Master's in Computer Science for the program of artificial intelligence. I already took a class in A.I. but I got a "W" on it. I wasn't doing very well and wanted to drop the class, I was also taking 20 credits at the time and didn't had the time to put the extra effort.

How will this be evaluated during my application for a Masters? Should I mention it or defend it anywhere in my application?

Some more background:
I am not really into excuses, but if it helps to better understand why I dropped it. About half the class, dropped the class because the professor was not very good. His grading was unfair, and also for me it felt he had a personal nemesis, because he was also my academic advisor and very often I would disagree in a respectful manner as to what I want to pursue in my degree. I didn't want my GPA to be affected by a C or even F. Also he was not a very effective teacher, but he seems to be very respected in the academia (he has some of his research cited 800+ times). Which I am sure he deserves.

EDIT: I already graduated and recently been working and had to use AI.

A withdrawal on a course that appears key to your masters' studies is probably a big deal.  It would be one thing if your W was in something more tangential to your onward studies.  But if you have withdrawn from a class in the exact same topic that you now want to study for your masters' degree, you really do need an explanation for it.  And it may hurt your chances.

Unfortunately, you don't have a great story to tell.  It may well be true that the professor was a poor teacher, unfair, and even biased against you.  But you don't really have any way to provide evidence of that.  The admissions committee will just be going on your word.  And unfortunately for you, those are the exact sort of things that poor students tend to say as excuses.  Saying such things is likely to reflect poorly on you rather than justify your W (especially if the professor is respected in the field).  I would avoid saying these things. If you get asked about it, focus on the fact that you were taking too many credits at the time and needed to cut back.

So, what are your options?

You could always just go for it.  This might be a negative on your record, but still you may get accepted into programs anyway--especially if the rest of your track record is excellent.  It would be less worrisome if you have other classes or projects that demonstrate your ability/interest in AI.
Try to fill the gap somehow.  Either by retaking the course, or doing some other research/work in the area to prepare for grad school.


Should I withdraw my paper because the editor is delaying the report? I am clearly disheartened by the editor's behaviour:

I sent a manuscript for peer review nearly three months back to an Elsevier journal with impact factor 0.625 in mathematics.

I inquired about the status of my manuscript after 1.5 months since it was still showing "With Editor " status.

The editor said review process is on and a decision can be obtained after 1 month.

After 1 month I again inquired about its status, to which the editor said that the report can be obtained in a few days.

But, since then, nearly 3 weeks have passed, but I did not get the report.
I have mailed the editor 2 times and the associate editor 1 time but no one replied.

The status is still showing With Editor.

Why is the editor behaving this way with me? I am waiting anxiously for my report as it matters a lot to me.

Are they avoiding my mails intentionally by not replying?

What is their aim? Do they want me to withdraw my paper? Should I withdraw my paper because the editor is behaving so badly with me?

NOTE: Also, if the editor is busy, why is the associate editor not replying?

My question is not a duplicate of submission review is taking too long because I never asked why my review process is taking long.

My question was

  If the Editor said that I will get a report in a few days , why did he not keep his/her word and now when I am sending him mails, why is he/she not responding?

The two questions are clearly different as far as my knowledge goes.

The situation is sub-optimal, but not as bad as you seem to think. Remember that being an editor to a scientific journal, even one published by Elsevier, is often a volunteer job. Moreover, the editors have no control over how long the reviewers take to review your article. (which reminds me...) So what they gave you was only a guess. If the guess was wrong, then that happens. What seems to worry you the most was the status of your paper. I would not worry about that. Sometimes editors use these function to track submission and sometimes they don't. If they do, then the status is probably fairly accurate, if they don't then it means nothing.

My suggestion is to think about publishing your article until you submit the article. After that you just forget about it (don't look at the journal website, don't think about it), because there is nothing you can do. Instead, focus on writing the next article. Only when you get your rejection letter, you start thinking about it again, and improve the paper and submit it to the next journal.


Visiting assistant professor position vs Post-doc position I have couple of offers for a visiting assistant professor (VAP) and for post-doc positions. I'm debating which to choose. I'm finalizing my PhD now at a top 50 R1 school in engineering. The VAP positions are at top 20 private liberal arts colleges. The two post-docs positions are one at my current university and another one at a top 30 R1 university. To be honest, I started applying for tenure track (TT) positions two months ago in February (I know it was already late! But I had some serious change of plans). I'm debating whether to go for a VAP or post-doc (at my school, since my research area is very new) position. I feel that I will get a better chance of getting some interviews during the next cycle of applying to TT positions (when I start applying in Aug/Sep.).

Here are few facts that might be useful;

My goal is to go for a TT position (R1 university).
Publication record is high (about 3 times higher than the average number of publications for a fresh PhD graduate in my field)
My current advisor is famous (he started my research area), basically I feel that my recommendation letters are good!
I'm not worried about salary/benefits (since both positions are not TT)
Received multiple awards/fellowships during my PhD
Proposal/Grant funding writing abilities - average (not very experienced)
I have heard from multiple people that getting a VAP for 1-2 years might look bad/questionable on a CV on the contrary to having a post-doc.

Any help/comments/experiences/suggestions shared will be much appreciated.

If your goal is to get a TT job at an R1 university, you would be a lunatic to choose a job with 3-3 teaching load with no research support over one that is research focused.  I'm extremely confused about why you're even asking this question.

EDIT: To specifically address "if getting a VAP job for a year would enhance my resume (to be able to compete for a TT position) over having a post-doc,"  the answer from everything I know is a resounding "no."  It will just look like you couldn't get a decent postdoc.  Maybe teaching 1 or 2 classes if you can arrange it with one of the postdocs would be a net positive, but the VAP job you're describing would be a disaster for your research, and that's what gets you the sort of job you say you want.  Maybe you're extremely productive and in a very in demand field, but if your research is good enough that you can take a year off (effectively) and still get a TT job at an R1 university, then you can potentially get an even better job (or be in a better negotiating position, or be in a better position to get tenure) if you keep your research up for another year.  Certainly very few people are so productive that they can afford to take such a huge risk.


Should I submit my paper to a different journal after not receiving any acknowledgment for five months? I submitted a paper to a low to mid-tier online-only journal in my field last January. I did not receive any acknowledgment from the editors that they received my paper and the journal has already published papers that were submitted after I submitted mine. Having been busy since January I forgot to ask the editors for an update. I was only able to send an email a week ago, and I still did not receive a reply. Should I submit my paper to a different journal or should I wait a bit more for a reply?

Give them another week, then decide.

Sending two messages within one week may be considered as pushy, I would try to avoid this. However, if you have serious concerns about the status of the paper it may be justified nevertheless. Whether or not your concerns are serious depends on the history so far: if you have not received any notification at all (via any submission system or similar), then maybe the paper actually got lost.

Personally, I would have contacted the editor earlier since in my field the review duration is 2-3 months -- of course, this may be different in your discipline. Some journals state certain statistics on their web page, such as the time from submission to the first decision. This gives you a hint what time spans you can expect until your paper is reviewed.


How to find the leading researchers in a new field I'm in computer sciences, in applied Machine Learning. I often have to switch applications and I find it cumbersome trying to discern the really good and bad works by doing a large survey.

Whenever you are new in a field, how would you direct your survey to find the people doing seminal work in the area, for example in the specific case of Latent Dirichlet Allocation in Computer Science, you can always go to a 2003 paper by Blei, Jordan and Ng. While if you are a seasoned researcher of the area, you already know this paper is relevant, how a newcomer would find such paper?

Do you ask experts in the area? Do you go by number of citations (I often find this deceptive, particularly in Bioinformatics)

I'm interested in this because I'm switching applications now, and I would like to know which group's work I should be following or which person's papers I should be reading.

Problem is that you hamstrung yourself by eliminating the only correct strategy: doing a long literature survey yourself. You wish to rely on proxies, and sometimes surveys can do that for you, but other people's opinions of "good" and "bad" are just that: opinions.

The only way to really get a sense of good and bad is to read a LOT, think a lot about what you read, discuss with people who might know more about the area, think a lot more, read more, and repeat.


In the United States, how customary is it for professors to not check their emails around Christmas? I hope I don't sound like I'm complaining, and I understand professors and academics are humans. My question is more of one of inquiry rather than venting. I have e-mailed a few professors for certain professional opportunities. This is not my first time doing so, and I am familiar with proper e-mail etiquette and how to write a message to minimize the chances of a glaring ignore. I have also received replies in the past. However, I have e-mailed a few professors about a week ago, and my inbox is crickets so far. On average, is it customary for academics to take a break from e-mailing during the Holiday break?

Yes, it's common. Many take a break from work entirely during this season. Some reduce their working hours to spend time with family, and only answer urgent email. Some may be traveling and have limited or no access to email. Some (like me) may be swamped with grading and other end-of-semester duties and are focusing on those at the moment.

If you haven't heard back by mid-January, try a polite follow-up then.


Can a professor do an internship? Can a professor (let's say a math professor) do something like an internship at a tech company during the summer as a way to keep their industry skills sharp / relevant? Does anyone ever do this?

Perhaps the word "internship" is not quite right, but the idea would be to show up, be useful for 6 weeks or so, then go back to the university and teach students relevant real-world skills they'll need in industry.

Yes, but they are usually called "visiting researchers" or, in some cases, "residents", rather than "interns". See for example Facebook, Microsoft, or Google.


How do I ask a professor whether his seminars & lectures will be available to students from other departments? I will apply for a PhD soon. I would be applying to the Politics department, but there is a professor in a different department who holds really interesting seminars on political topics. However, as I said, he is not affiliated at all with this department. How do I ask him / how could I phrase this best?

PS: My question is not whether I can attend his lectures as a guest -I would love to take these seminars for credit, if I can. I just don't know whether that's an option, or whether students from the politics department will be allowed in these lectures/seminars.

The answer to your question is easy. Simply ask:

  I am very interested by your lectures. Can I attend them as a student in the politics department?

The professor, however, is probably not the best resource to answer your question, especially if you want to enroll in the course. You should enquire at your future department what is allowed and what is not. Rules can vary between departments and programs.


What to teach first: theory or practice? The educational system in which I have studied focuses on teaching the theory/abstract theoretical courses before the applications.

For example, I spent the first 1-2 years of a 5-year engineering program only studying Mathematics, Physics and other basic courses before even getting any hint what the applied problems we will eventually try to solve are. In terms of tools, I first learned and programmed the individual methods and then I used "real-life" software for the first time.

Now, having seen applications, I look back to my basic courses and I think "that abstract topic was actually much simpler than I originally thought!".
It feels like I was just stupid to not be able to fully understand or get interested enough into the abstract topics.

I would feel much better if my university has made me first work on some easy applications, trying to understand the context, the difficulties and the possibilities, then dive into theory and then have the advanced applications that require advanced theory. A kind of "iterative model". I understand that this would probably take more time.

However, I see that university education keeps being like this in the universities I have studied into (Greece and Germany). Strong theory first, applications later. Traditional, "sequential" model.

Does my "iterative model" observation, as a student, make sense from a teaching perspective? What is the current situation and trend in more "progressive" educational systems? If it is not already applied, why not?

It isn't really a question of either or in terms of theory and practice. Instead, what is needed is theory and practice happening simultaneously in the classroom. The students learn a concept and then they used it immediately in some sort of authentic assessment. To have to what 1-2 years to use any sort of new knowledge is difficult for the average young adult learner and nearly impossible for a mature adult learner. Knowledge retention is most effect through teaching it to others and followed next by the application of it.

Within education, there is a big emphasis on learning by doing or being an active learning. This can take many forms such as the use of projects, problem-solving, presentations, etc. The point is that the students need to learn through actually doing or producing something through some sort of authentic real-world application. The real-world application creates the relevancy that most students need in order to process whatever it is that they are learning. This is particularly true for inexperienced students who have zero practical knowledge.

A major exception to this is the experienced student who returns to gain theoretical insights into their career. For example, if a teacher returns to school for a master's in education, they often experiences many "aha" moments when they see a connection between a theoretically concept and something that happened when they were teaching. Since these people already possess practical knowledge they are even better able to appreciate theoretical knowledge and create a bridge between the two.


Unexpected Extra Travel Costs and Grants When traveling, there are many things that can possibly happen or go wrong that would require extra money to fix.  While these things may not be directly related to the research travel one is doing, these expenses would not pop up if you weren't traveling.

For example, if one gets stuck in the airport on the way back to one's home institution, you may need to get an extra night at a hotel before you go home.

The question is the following: When is it appropriate to claim such an expense on one's grant?

There are clearly varying levels of such events. One is something out of your control like weather pushing your flight back a day. Some are completely in your control and you messed up, e.g.,  you miss your flight and need to pay a fee to get on a later flight. Others are due to scheduling conflicts and new plans arising, e.g., another talking engagement shows up and one needs to pay the flight change fee in order to make sure one can present at both conferences.

Are all/some of these scenarios appropriate for claiming against a grant or asking reimbursement for?

These things happen, and as long as the expenses are reasonable, they should be covered by any reasonable funding body. It is a good idea to make a phone call to see whether you are permitted to spend the money, or at least to find out what budget limitations you have.

For instance, the other day my plane was diverted to a different airport. The only way I could make the PhD defence on time was using a taxi. So I took the 80 km trip and paid the 230 euro and fully expect that I'll get this money back.

If I had have purchased a used car to get me to the defence and a bottle of whisky for pain and suffering, I wouldn't expect to get that money back.


Possibility of negotiating a better contract if I am offered an asst prof position? I attended an interview last week for an asst prof position in math in a university in the UK that is much lower ranked than the universities where I did my PhD and postdocs, for instance, my PhD university is one of the top 20 worldwide whereas this university is ranked in the 300-350 bracket. The university is in the city where my girlfriend works hence why I decided to at least apply for the job but I am in no way going to jeopardise my career just to live in the same city as my gf if I decide this is position is not a good move.

Do you think that if I was offered the position I could negotiate a better contract? For example, if I was to request that instead of coming it at the very bottom of asst prof scale, I come in several ranks higher?

I would be in the running for asst profs jobs in much higher ranked institutions, or I could make alot more money by going to industry which many of former PhD colleagues have done - so from my perpsective if I am to sacrifice positions at better institutions/higher salaries there would have to be some compensation. This is a very big sacrifice since, as far as I understand it, you can step down in the university rankings as much as you want to take a job but you won't be stepping back up..and I imagine it will be much harder to apply for and get funding, etc. coming from a much lower ranked place.

So do you think it is possible to obtain a better contract or is the academic hiring system so rigid in general that there is no room for manoeuvre here and I would be forced to come in at the bottom rung of the ladder?

In the UK, there is typically much less negotiation of entry-level academic contracts, compared to the US market, or general stories of how it was in past. Full professors still can negotiate their contracts, but assuming that it is your first permanent post, I would be surprised if the University would engage in a negotiation with you. Typically, the universities in the UK will match your current academic salary or offer you to start one spine point above it. In exceptional circumstances they can offer two spine points, but "I am making a sacrifice here for you guys" is hardly going to count as a good reason. You are expected to compare your options, and if you indeed have a better deal elsewhere, you'd better take it. Comparing their offer with hypothetical offers you could have got from some industry is likely not going to work.

But before all this becomes a real problem, you need to get their offer first. And to get there you typically would need to pass through the interview and convince the panel that you understand what you are getting into and you are genuinely interested in the opportunity as it is offered to you. If you are less than enthusiastic about this particular university and/or the conditions they offer, I would suggest to try and discuss this during the interview, so that the panel can make an informed decision whether to offer this job to you (and perhaps agree on your conditions) or another candidate. If you confirm your interest in the position during the interview and try to re-negotiate the conditions afterwards, it is quite likely that after some discussion the post will be unfilled and the position has to be re-advertised, which is really quite frustrating to everyone involved.


How should I list an unfinished bachelor thesis in my application for a Master's programme? I am currently a final year undergraduate but I haven't finished working on my thesis yet. (I'm currently working on it nonetheless)

However a professor of mine told me to put it in the CV since it is also very related to the Master's programme.

How could I mention that it is not finished in the CV?

Writing "thesis: < title >" in the CV
 without further information looks like I have at least submitted it.

I would list the title of the thesis along with an expected completion date.

Depending on the format of your CV, this may just be the year, or, if you know the exact deadline, the date in Month, Year or DD/MM/YY format (the specifics of your long date formatting is country-dependent of course).

The listing on the CV might look something like

  Bachelors' Thesis: "My Awesome Thesis Title Goes Here." May 2017

Or

  "My Awesome Thesis Title Goes Here." (Bachelors' Thesis, expected
  completion date 30/05/17)

If you are submitting some form of covering letter as part of your application, it would also be a good idea to talk about your thesis there and also note that it is not yet complete. However, I think the admissions committee would be aware that if you are a current undergraduate student that your thesis is likely to be unfinished at this point. Good luck with your application!


Is it okay to work on a problem which is incremental as your first Ph.D problem? I am a Ph.D. student in theoretical computer science. I have recently come across one problem on which somebody has already done work, but in that work I figured out one problem which may be small (I don’t how significant it is). I asked my colleagues about this, and some of them suggested me to pick a new problem for your first Ph.D. problem. I am in confusion what to do.

My question is: Is it okay to work on a problem which is incremental as your first Ph.D problem? Incremental in my context simply means designing a faster algorithm.

Yes!

Your goal for your first problem is just to publish something. It doesn’t have to be significant. It doesn’t have to be in a top conference. It doesn’t have to be related to your eventual thesis topic. It doesn’t even have to be in the same subfield as anything else you publish in the future. Just publish something.

This is just getting you used to the process of writing and revising and submitting and being frustrated by bad reviews and rerevising and seeing the results in print, so that none of that stuff is a barrier later.  This is inoculation against the inevitable future Impostor Syndrome telling you that you can’t do this, because you already did this.


Should I contact the editor-in-chief about a senior editor's lack of communication? I submitted a paper to the top journal in my field. The journal's home page sets 120 days for a decision as a goal. Recent stats suggest 60 days to initial decision is more typical.

It has now been seven months, with no word. (The paper sat in the queue marked "Awaiting AE assignment" for two months, and has since been marked "Under review".)

Colleagues have varied in their recommendations about approaching the SE [Senior Editor] with a polite query as to when the review might be complete. Some advised strongly against it, due to some bad experiences with quick rejections following such a query. Others, typically more senior (and tenured) people, advocate a "wait and see" approach. Recently, I was able to speak with the former EIC [Editor-in-Chief] of a peer journal (a different journal, also at the top of my field), who very candidly advised me to contact the SE immediately about a decision. On his advice, I did so.

It has been two weeks without any sort of response with the SE.

I have chatted with other editors at this journal (AEs [Associate Editors] and SEs), and concluded this is likely a continuing issue with this particular SE. He is purportedly exceptional in his reviews, advice, and decisions, but not so much with timeliness.

As a very junior person, the status of this paper is very important for job prospects. My mentor (and co-author) takes something of a "throw me into the deep end" approach, and invites me to solve the issue without his intervention.

So, my questions are these: How long should I wait before contacting the SE again? Is there a point that I should contact the EIC or managing editor? (For context, as I understand it, the managing editor is a very junior person, effectively an administrative assistant to the EIC.)

May be similar to Is it wise to contact the editor of a journals with my concerns regarding the length of the acceptance process?, and perhaps How to let a journal know that its submission process is very painful?, as well as some others, but different in seeking advice for escalation beyond SE.

Edited to clarify EIC [Editor-in-Chief], SE [Senior Editor], AE [Associate Editor]. As I understand, SE is assigned by managing editor, based on content and submission letter. SE assigns a blind [?] AE. AE assigns/recruits blind reviewers.

The reviews are already 3 months overdue past the deadline. You have every right to ask for a progress update, if only to remind the editor in charge of your paper that you're still waiting.

I would write to that editor again, and if you don't get anything back write to him again with a CC: to the Editor-in-Chief.


How to address the person being recommended in a recommendation letter? How should one "address" the person for whom I am writing a recommendation letter in the letter?

Scenario:

I have known John Doe for many years and am familiar with his work. We address each other on a first name basis. I've been asked to write a letter supporting John's application. When I write about him, should I write

  Dr [or Mr, in case of undergraduates] Doe's works are well-written ...

or can I get away with

  John's works are well-written ...

Personally I feel a bit strange writing Dr Doe for someone I know so well, but I wonder if it is better to err on the more formal side?

For what it is worth, the field is Mathematics. And for future reference, I do not want to limit the question to a particular level of application (for graduate school, fellowships, or for jobs); I suspect that shouldn't make a difference in the answer, but if it does, feel free to indicate.

I have seen both used in recommendation letters, regardless of the strength of the recommendation letter itself. I would, myself, recommend Dr. John Doe / Dr. Doe for most professional relationships, except when it is clear that you have formed a close professional relationship (PhD student, or long-term collaborator or post-doc). In case you go for the surname, I would still use the full name at the first mention:

  Dr. John Doe was a student of mine at the University of X, where I teach Y, …. He later joined my research group as a Masters, then PhD student. John is an extremely bright student, …

(Of course, that's merely an example and not a good letter wording, so do not look at the wording itself, only the use of names…)


What solutions exist to store data in text files and future-proof against tampering? A recent question in Information and Security Stack Exchange,

  How to know whether a textfile has been edited or tampered with

raises a very good point: if one wants to archive experimental data in an open, text-based format, in the long term, it is desirable to have tools to prevent the tampering of the files, or at least detect the tampering if and when it happens.

The answers at infosec are good, but they feel somewhat abstract and hard to implement for a busy PI whose hands are already full trying to run a research lab. It may be, on the other hand, that solutions already exist that fulfil at least some of the requirements, or that they will appear not too long in the future; it's certainly reasonable to suspect that some form of tamper-resistant data or lab-book signature scheme is already in use at least in commercial research organizations.

This question is relatively hard to pose correctly, as there is an inherent vagueness in the requirements, and it is probably better to keep it general. The main problem is, given a set of text-based data files, how to signatures, or similar devices, that can be used in the future to provide guarantees that the data has not been tampered with. Are there any specific solutions that will do this in an accessible way?

In addition to good recommendations on the InfoSec SE site, some of which are not that difficult to implement (for example, digital signing), I would suggest another rather straightforward solution (unless your data is extremely large or extremely sensitive): simply use one of Git repositories, such as GitHub or GitLab, or research data repositories, such as Zenodo or figshare.

Git and Git-based services now support large files, plus you will have an added benefit of versioning for data files that you can match with your research workflows to enable reproducibility.

Check my related answer on some arguments for potential preference for Zenodo vs. figshare.


Etiquette for an initial meeting with a prospective advisor: What is expected of the student? Assuming that one has begun a PhD program at a university which allows a student to choose an advisor after his/her first year in the program and the student has narrowed down on a couple of potential advisors and has taken AT LEAST one course with each of his potential advisors:

What should the student take to the first meet? A rough research idea, summary
of the professor's important papers or otherwise?

Note: I have made 5 separate questions as suggested (As opposed to the single one which I started off with)

For an initial meeting, I would take an general idea of the kinds of things you'd like to do in a particular advisor's group, a sense of what the advisor works on—you don't necessarily have to have read papers in advance, and an open mind. That said, you'll make a better impression if you have read a few recent papers, and have a few intelligent questions to ask. It will pique the advisor's interest, and show your sincerity.

As for coming in with ideas for a research project, this depends a lot on how the project will be funded. If you have your own fellowship and can design your own project, then you should definitely have an idea or two ready. On the other hand, if you will be funded by an existing research grant within the group, your choice of projects will be more constrained.

One final note—I would say that it's definitely not required that you take a course with an advisor before considering them as a research advisor. If that were the case, I would have been on a completely different career path than the one I'm on now, as I'd be working for my fourth-choice advisor (who was the only one I took a class with before choosing a research group!).


Is pseudonymous publication ethical? From this MathOverflow question:

  William Sealy Gosset published a result under the pseudonym Student. (Because his employer, the Guinness brewing company, did not allow their employees to publish for fear of divulging trade secrets.)

Why isn't publishing under a pseudonym a breach of academic ethics? It seems that the common idea is that publishing under a pseudonym is ethical, unless they are deliberately used with intention to defraud or deceive. But, given that we don't know who a pseudonymous author is, how can his peers have any trust in that (or even check it)?

The worth of scientific work is in the content, not in who wrote it. Therefore, I think publishing under a pseudonym is not necessarily unethical. In the example the OP presented the author was prevented from publishing if he used his own name. If the research was sound and reproducible, I would be fine with this. In practice I would like to know who wrote the paper.


Is it a good idea to postdocs that are less than a year? I've noticed that there are a lot of postdocs postings that offer fixed-term contracts for 12 months and sometimes less (I did find 8 months). I'm looking for a postdoc position as my first post-PhD job and I don't know if I should also consider those. For the short-term contract, what's the usual story? do they really expect you to publish in just 8 months?

Typically very short (<1yr) positions are offered because the PI only has money to pay for a few months' postdoc time. This can arise for a variety of reasons, but the most common is probably that they obtained a grant to pay for (say) a 3-year postdoc, and then hired someone who found a new job after two-and-a-bit years. This is an awkward situation: often funding agencies place strict time limits for money to be spent, so one may be faced with the challenge of getting rid of a substantial pile of cash quickly, and hiring someone is the only realistic way to do this.
Related, but distinct: sometimes PIs will choose to spend the dregs of a grant on employing a graduating PhD student for a few months after they complete their thesis. The length of position offered is usually directly governed by the amount of money left in the bank. In such cases it may be necessary to 'advertise' the job to satisfy employment regulations and/or policies.
Unless you are already involved in a project, it is difficult to achieve much in a postdoc that lasts less than a year. Inevitably you lose time at the start getting settled in (especially if you have to move to a new city), and you will be busy applying for new jobs and attending interviews. PIs' expectations no doubt differ, but I think it is unreasonable to expect much to come out of such a short position.
Often PIs in this situation will be applying for follow-on funding, so there is a chance that the position will ultimately be extended to a decent length. However, you should not count on this happening.
If you see an advert of this sort, I think it is reasonable to contact the PI and ask for an explanation of the circumstances, and how they envisage things working. Personally, I would only apply for such positions if the alternative were unemployment.


Took GRE two times, same scores with minor differences - worth sending both? I took the GRE for the 2nd time recently and unfortunately, after 4 months of studying (again for the 2nd summer in a row), received the exact same score overall as my score last summer.

Last summer, I got a 157 on math, 154 on verbal, and 5 on the essay. Recently, I got a 157 on math, 153 on verbal, and a 6 on the essay.

Is it worth sending both GRE scores to the graduate schools I'm applying to (I know they all, for the ones that accept the GRE, accept multiple scores). Even if they don't superscore, I feel like it may show that I tried to increase my score and went out of my way to take it a second time...also a higher essay score may be worthy to show for. What do you think? It's a very small matter, but I feel that it may be slightly beneficial at best in terms of my overall application, so why not?

By the way, I'm applying to biomedical neuroscience PhD programs that focus on disease therapeutics.

Thanks for your input!

I actually think that sending both tests would be detrimental for your application:

it decreases the ratio of signal to noise in your application
[opinion based] it shows the lack of improvement in your math and verbal scores over the year (which would be my interpretation if both results are sent) as opposed to your intent to show the will to improve
generally adds confusion

Since your most recent result is in all aspects better/equal (I don't count 153/154 to be different, while 6 on the essay is much better than 5) than the previous one, I strongly suggest sending only the newest GRE score.