Improving on a scientific paper (with source code) - publication of our work possible? I and my students are working on a paper that has associated source code in GitHub. We are planning to change the architecture of the Deep Learning Network they have used, and check to see if we would get better results. Would we be able to do any kind of publication of our work by citing the paper we had used?

Yes: You can publish work that improves upon earlier results.

Whether changing the architecture of a Deep Learning Network will achieve better results is, of course, an open problem. Whether improvements are sufficient to merit publication is also an open problem.

In theory, negative results - e.g., we changed the architecture and didn't get better results - are publishable too. But, such results aren't published as often. I think you'd need a surprising-factor, e.g., if better results could be expected from such a change, but aren't achieved, especially if the reason they aren't achieved can be identified.


Quitting a PhD program after four years and applying elsewhere I am a fourth year graduate student at a tier 1 research university in the US. I had lot of hiccups in getting started with my research. Our program is rotation bases where you rotate with your potential PIs for a semester (or more). I decided to rotate with Prof. A and continued it for another semester. However, in the summer of the year I was transitioning into my second year, I went to Prof. B to do my last rotation. Prof. B had a more concrete project that I worked on and I was super productive under him so I decided to join Prof. B's lab permanently. However, Prof. A was not happy about this since I had done two rotations with him.

In my third semester Prof. B decided to leave academia and moved to industry. I was given an option of quitting with a Masters or joining another PI. I chose to find a new PI. My research focus was in a particular area that only Prof. A and Prof. B studied. Our department is anyway too small with only 6 faculty who work on completely different areas. So, after being without a PI for almost a semester I decided to approach Prof. A to see if I could join his lab. He was not convinced initially. I had to provide detailed account of things I had worked on with Prof. B. In one of such early meetings, he told me "I don't have to do this. sufficient number of students have graduated from my lab and I have a tenure now.". But eventually, he decided to let me in his lab. Since we both didn't have a concrete project in mind, he suggested I write a review article on the project I had previously been working on. That did not go well. I wasted a semester studying that area in depth, but went in a tangential direction and couldn't finish the review. However, a new project came up through a collaborator and I was assigned to finish it. However, there were very limited questions that could be answered and my progress left him dissatisfied. I was told I could do 'cool things' with the data, without ever being told what these 'cool' things could be given the limited nature of data. In this process, I got another project to work on which I saw as being my main contribution to my field. However my PI has always found my methods to be 'too complicated'.

In this entire process, my realtions with my PI has always been deteriorating. I have been told "I am smarter than you", "I am not interested in your sloppy work", "Don't waste my time with your bullshit". My requests to talk about our method have lately been ignored.

I wanted to work in academia and I want to finish my PhD. However when I think about the relation I share with my PI has forced me to wonder if I even finish my PhD, his letter of recommendation will be a negative one, probably killing my career anyway. My post sounds toxic, but so has been my relation to my PI. I had to seek professional counselling a year back. With the relation we share currently, I don't let it affect my work. However, I am also not at peace with it in my mind.

Hence, I am considering quitting and applying elsewhere. However, I will need letters of recommendation from him to do that. How do I present my case? I have a decent GPA in undergrad/grad schools. In these four years, I was also able to enrol for a Masters in a related field in the same school.

Consult Professor B; he thinks highly of you, and can suggest someone for you to work with, who is not professor A. This may entail moving elsewhere.


How many rejected papers does it take to get an accepted paper? Today I received my first rejected paper.

The committee of 2 people left some good points but at the end they didn't get the point of my theme. It took me 3 months to write this paper for the Requirements Engineering Conference in Lisbon, Portugal.

I talked to 2 PhD students and they said that this takes time and passion. They told me that the average of rejected papers/journals per capita is 7. Do you agree with this average?

This varies depending on a huge number of factors.  The venues you select to submit your work, the quality of the work, whether the work is described well or penalized because it is written badly, misses important related work, or many other factors.  And it no doubt depends on field as well.

I would however say that the idea that you submit 7 times for each time you get something published means you're setting your sights too high.  In Computer Science, for instance, probably most conferences have an acceptance ratio of 4:1 or 5:1, perhaps 6:1, at worst.  But then many others have much high acceptance ratios, so I would think the mean acceptance rate is 4:1 or 3:1.  In my own experience most papers have gotten in either the first time or the second.  One took 3, and another time I stopped trying to publish the work, but the average would be around 1.5-2 at most.

Whatever the ratio is in your field, by all means don't get too stressed over your first rejection.  It's part of the process!  And work with your advisor to find appropriate targets that are realistic.


When should cited author names be included in the substantive, rather than parenthetical, part of a citing sentence? To give credit where credit is due I strive to make it clear where ideas of others, which I use/refer to in my papers/work, are from. For this I cite and quote and this question is about the correct form to do so. Unfortunately I lack the words to describe the problem and like to give two examples.

  There is this idea (Person(s) 1984).

  It has been this idea of Person(s) (1994).

While I know that it is possible to use (1.) form I often also encounter the cases in which I would rather prefer to phrase it in the style of (2.) in which the Person(s) cited appear as an actual word of the sentence. Now this is where I am lost what to do with the year of the actual cited paper/book/etc of this Person(s).

The question therefore:

Is it possible/legitimate/"okay" to refer to previous works/others by telling about those people directly inside of a sentence (meaning appearing as a part of the sentence)?

additionally:

if yes, how?

if no, reason why not possible/"okay"?

Both ways are equally acceptable and used in separate instances. Basically if the author(s) names occur in the sentence type (2) should be used and if the name(s) are not then type (1) should be used. The question is then when the two forms result.

Type (1) is a more passive form used when you, for example, are describing general background where the specific reference might not be key. The form is quite common (but not exclusive) to the introduction section. The sense is that the information is more distant from your own study. Version (2) is used when the cited studies are building the story and is closer to your work and thus more important for understanding the details of your study. A good example may be in the discussion where your results are compared with other specific studies. This is just a generalization since both are useful in all parts of a research article.


Getting into a topic one is barely familiar with? Intro

For an upcoming project I have to get into a new topic of research which is not similar to anything I have worked so far. Furthermore, this project requires learning new programming language(s) and simulation environments. And in the end a software implementation and a final report has to be written

About the topic

The whole topic is about wireless mobile communication, the basics of communication technologies which are used in this topic are the same with the usual mobile wireless technologies I've learned before. However, the dynamics of the mobility are fairly different. The clustering algorithms used are not typical.

The essential question

How do I tackle such a situation, where multiple new things have to be learned before the final results are delivered. I separate the things I have to learn into

Prerequisites: programming languages, simulation environment, relation between them and the topic basics
Main work: learning the essential elements of the topic and becoming fluent in them

Past experiences

In the past I have usually worked on research topics which I have fulfilled the prerequisites for. So, I would tackle the topic following these steps:

Read broader literature: Surveys
Read literature about the specific problem
Implement if there is something to be done
Write final report

In this case I am a bit lost. I don't know where should I start from. That's why I need help from more experienced researchers. Compared to the list I provided above, step 3 is quite more complicated in this case, as I am not familiar with the programming language.

What I plan to do

I want to follow the following steps in order to get into this topic

Fulfill the prerequisites: get familiar with the required programming languages and simulation environments. Coupling between them etc. Do some exercises until I feel confident.
Start reading broad literature: Surveys
Focus on the specific problem: Read specific literature
Start implementation
Write the final report

I am not quite sure if these steps are OK. Sometimes I get confused and I want to move 4 -> 2, 2 -> 3, 3 -> 4 and maybe parallelize something there with step 5.

Any suggestions would be greatly appreciated. I feel so overwhelmed by this topic and need urgent help :(.

While your concern is perfectly valid (been there myself more than a few times), you should probably consider and accept that this is the way you are going to learn new things for most professional endeavors. This is how things work out of college; e.g. think about this: are you able to foresee what technologies and concepts are going to be required for your next project? And even if you could name them, could you set aside enough time for mastering them to be prepared for the next assignment?

As I see it, you already have a sound plan, I would stick to it. I would, however, recommend that you not get too engaged in just familiarizing yourself with the new environment. Sure, take some time to get some grip on it, but once you are got the basics, I suggest proceeding with your plan. One major asset of your assignment is going to be your new acquired skills, but that mastery will come in small portions along the whole road of the project. I find it unlikely (for students and professionals alike) to be able to learn a new paradigm in a reasonable time, without some means to guide the effort, e.g. class projects, so, instead of trying to get to the bottom immediately, get the basics and learn the rest along the way.

Other than that, as I said before, your plan is sound, just don't let the fear of the unknown overwhelm you into panic.


Transitioning from Electrical Engineering to Astronomy/Physics I have a Master's Degree in Electrical Engineering(Fresh Graduate with emphasis on Electronics/RF-Microwaves). I'm thinking Engineering is not for me and want to pursue Astronomy/Physics.

How hard is it to do so?
What ways I can transition?
How can I be sure that the fascination with the subject is a genuine interest?

Thank you

The gap from electrical engineering to astronomy or even physics is big for a PhD. The other way around it's easier as physicists anyway specialize after master in a distinct topic, while electrical engineering is already quite specialized. Astrophysics is a field of physics that needs a thorough background in most of the physical theories apart from condensed matter physics. You would have to catch up a quite huge background. Only option I see is to dive into a very specialized PhD topic like, e.g. pulsar radiation or solar physics and trying to do simulations/data analysis on such systems. Other topics will need a lot of self-teaching and I'm not sure, even if you would be willing to spend this time, if supervisors or professors would like to offer you this time with alternative candidates. And many physics students want to get tenure in astrophysics, the competition is much higher in this field than in big fields like condensed matter physics.

I would rather suggest to you to look into topics and fields of condensed matter physics like spintronics, quantum sensing, quantum computing. Electrical engineers sometimes will have here an advantage over candidate with a master in physics concerning a distinct topic/task like circuitry development for superconducting quantum computers or quantum sensors.


What exactly is “quantification”? As I’m writing my final words within a research paper, I was curious regarding the term quantification of results.

Namely I’ve performed a correlation analysis in a quasi-experiment. The research is quantitative and purely related to software engineering.

My findings were that the two measured variables do correlate. Now, before I start getting into anything, what exactly specifies quantifying results of e.g. this correlation analysis?

There are two ways to report your findings:  Qualitatively and Quantitatively.

Qualitatively is just using words.  So you could say "we see good correlation between the datasets in the two experiments, but experiment A shows a slight bias at small time."

Quantitative analysis uses numbers.  You could say instead "Correlation analysis shows both datasets are correlated with p < 0.05.  Experiment A shows a bias of 0.1 at times less than one hour, and the correlation coefficient of both datasets using partial data fitting (I just made that up) is 0.13 with a t-critical value of 0.2.


Best practices for dissertation committees to review chapters? From talking to colleagues in a variety of fields and different institutions, there seems to be a huge variability in the ways committees handle their responsibilities of reviewing dissertation chapters. I would like to know two things:

What do you consider the best practices for advisors, other committee members, and candidates in order to move the dissertation writing along efficiently?
Does the Journal Review policy (specified below) seem reasonable to you?

  Journal Review Method

  In this model, the dissertation advisor treats his or her role as the
  chair of the candidate's committee as if he or she were the editor of
  a journal and the dissertation chapters articles submitted for review.
  The student submits a chapter to the advisor who decides whether it is
  ready to send for review. If it is, then the advisor sends the chapter
  to committee members for review. The committee members make a brief
  (2-4 page) report to the advisor that either: accepts the chapter as
  is, accepts it pending minor revisions, rejects it pending major
  revisions, or rejects the chapter entirely. The advisor then makes the
  final determination as to the status of the chapter. It will be the
  advisor's responsibility to make sure other committee members submit
  their reports in a timely fashion. The defense is held when the
  advisor judges all of the chapters to be "accepted".

  The primary benefits of this policy are that it creates a clear
  organizational structure which allows candidates to receive prompt,
  actionable feedback on their work.

The policy is straight forward but an open question is what use a complete reject means if the advisor has deemed the chapter as passable. As I see it the advisor has (should have) both the insight into the details of the problem and research as well as general knowledge of academic expectations to deem when a manuscript is in shape for passing on. If a committee member does not think this is right then the question still remains who may be right and who may be wrong? Is the decision by vote in the end since there will likely be three or five persons involved in reading the chapters? In my system it is possible for a student to defend even if the advisor or committee member advise against it. Only fools do but it is possible. It is however, still possible for committee members to disagree but usually when issues arise it is because the student-advisor communication has failed for one or the other reason.

So in my view the "journal review method" is a good start but you also need to consider what will happen if there is disagreement and how to possibly weigh the input. Do all committee members have equal weight in all aspects or are they experts in some parts and therefore carry more weight in those chapters than in others. I think the system requires some tweaking in order to accommodate the clear differences that exist between a journal publications and a thesis (sensu monograph) where a thesis typically contains larger quantities of more detailed information than would be possible in a published paper.

As a side point, in my system where paper based theses are the norm, it is hard to "reject" a published paper; one can disagree but something that has passed peer review (albeit a poor one) has still passed. The key pint is thus the overall quality of the work and of the emerging scientist behind it. This i snot necessarily covered by the "journal review method" alone.


Is referencing online solution acceptable when completing assignments I'm not sure if I'm overthinking this.

Recently I had an assignment that is intended to be completed individually in which I cannot understand one of the questions at all. Lectures didn't help as the question assumed we have known some mathematical concepts before this class.

So I searched online for solutions because I realized that I would have learned nothing by keep looking at the question myself. And not surprisingly I found a solution.

I read through it, understood the solution, and wrote in my own words on the assignment paper. However since it is a simple proof my solution is essentially the same, so I cited the webpage and explained that I have written this proof after reading through the solution.

I know this does not constitute plagiarism. What could I have done better in this situation?

This depends on the rules of the course and has no general answer. For some courses and for some assignments within them, this would be expected. In others, forbidden. Only the instructor can give you guidance.

But, you did the right thing in citing it. You were honest. Also, you learned something, which was the point of the assignment. But perhaps you didn't learn the right thing, which may have been the point: working through to a solution on your own.

The rules of a course should be clear. It is a problem when they aren't. But if challenged on this, just stress your honesty in citing your source. And follow the rules as you then understand them. But, sadly, instructors sometimes have unspoken expectations.

If I were your professor, and had neglected to make the ground rules clear, I'd accept your work, given the citation, but also caution you about future work if I'd rather you came to me instead of external sources. A professor can sometimes give a minimal hint to get a student over a block, but still allow for deeper learning to occur than can be done when searching out solutions. But I would also have to publish the ground rules.


Are participations in competitions well recognized for a Ph.D. application? During undergrad, students can face several opportunities, ranging from participation in (1) research groups, (2) study/training for competitions, (3) internships, (4) opening start-ups with colleagues (the latter is becoming very common these days), but I wonder, what is really important, for a Ph.D. application/admission...

By competition I mean ones like: INTEL GLOBAL CHALLENGE (VC), ACM ICPC, IMAGINE CUP (examples from the Comp. Sci. field, and Business, but indeed there may be a bunch of these in other fields, that I don't know)

Talking about (1) and (2) aforementioned...

If a student stays a long time during his/her undergrad in a (world-class) research group, he/she is likely to have the opportunity to publish a bunch of papers (some of these might be good, well-referenced, etc; some of these might be not as good), and meet some good researchers around the world, and so on; it really required dedication.

On the other hand, take part into a training class for competitions (that requires dedication, as well) may lead students to gains in terms of working in group, time-boxed activities, etc, as well as to face the opportunity of proposing solutions for real-world problems, and so on.

It is really tough to do both, in order to have great results, since in both cases time and dedication is mandatory. Indeed, there are some "outliers" students that can do both in a very good way, but I'm trying to generalize my assumption, by considering "average" students.

Hence, it's known that good papers have a great influence on the Ph.D. admission (despite of other well-known recommendations, e.g., a great GRE, good recom. letters, and so on), but I'd like to know if (and how) the universities consider students who dedicated their time to join this kind of competitions, obtaining some prizes, as a consequence, etc.

Competitions can be valuable evidence of achievement, but they have to be not just widely recognized, but also really relevant to the field.  (Nobody cares if you're a chess champion, since you aren't going to grad school in chess, and the fact that it involves hard work and talent will not help your case; if anything, it will be viewed as a potential distraction that may cause trouble in the future.)  The best case is if some of the faculty once participated in the same competition.  Then they will know exactly what's involved and what success means.  The next best case is if some of their current students participated.  Otherwise, it will mean very little, unless your recommenders somehow make a strong case for its importance.

As a test case, let's think about the Putnam examination, which is the most prestigious math contest for undergraduates in the US and Canada.  Doing well on the Putnam exam is very valuable in math grad school applications, but even being one of the winners is not a guarantee of admission.  The big advantage of the Putnam is that it gives objective evidence of talent compared with a nationwide pool, but the disadvantage is that solving contest problem is really not the same thing as doing research.  If an undergraduate writes a paper a faculty member would really be proud of having written, then it looks better than winning the Putnam exam, but most undergraduate papers do not rise to that level and may not be as impressive as winning the exam.  It's hard to quantify this trade-off, but I would definitely not advise anyone to neglect research opportunities in order to prepare better for the Putnam.  Ultimately, graduate school is about research, and admissions committees sometimes worry about applicants who look more interested in competitions than research.

The Mathematical Contest in Modeling may be more along the lines of the contests you mention: it's a multi-day, team-based contest.  My impression is that it carries less weight in admissions decisions than the Putnam exam does.  Being able to help organize and train a winning team has real value, but it won't play much of a role in graduate admissions.


Using the names of the teachers in Personal Statement? Is it ok to use the names of my ex or recent professors in the personal statement? Of course in positive context (how they influenced me etc.) I am not from the USA and in my country it is quite uncommon to write essays like that, so I do not know if it would be ok to use the names.

There is no reason of ethics or custom to prevent you from using the names of professors in your personal statement.  Remember, however, that the personal statement needs to be about you, not about your professors, and choose accordingly whether to talk about a particular professor.

Thus, for example:

If you are talking about a research experience that you had as an undergraduate, then the name of the professor that you worked with is quite germane, and likely to be one of your references in any case.
If you are talking about a class that inspired you, then the class and the professor are not particularly interesting for the statement: instead what is interesting is what that inspiration has caused you to do.


How should I plan my course schedule given that my wife is due to give birth during the semester? I have been teaching for a few years at my university,
and have mostly gotten into the rhythm of teaching and doing research.

This semester, I am teaching two courses.
What is different this semester is that
I am faced with the happy but unfamiliar circumstance
that my wife is due to give birth during the semester.

Question: How should I plan my course schedule around the birth of our baby?

Here are some of the issues that I have considered:

The unpredictability of the birth date.
We are expecting that our baby will be delivered naturally.
While we were given an expected due date by the doctors,
we don't really know when the contractions will start,
when we will go to the hospital,
how long the labor will be before the baby is born, etc.
The day of week effect.
I am teaching on Mondays and Tuesdays.

If my wife goes into labor on Saturday, Sunday, Monday, or Tuesday,
I will probably be needed to help my wife give birth or recover,
so I plan to cancel class.
If my wife goes into labor on Wednesday, Thursday, or Friday,
we will probably be in a good enough situation
that I can teach on Monday or Tuesday.
But should I cancel class regardless?

What to communicate to students.
If my wife suddenly goes into labor,
I may have to suddenly cancel class.
This could happen shortly before the class starts,
or even possibly in the middle of the class.
Should I communicate any information about my wife's pregnancy
and the baby's expected due date to my students beforehand?

I would appreciate wise advice about
how to plan my course schedule
in a way that balances my family's needs and the students' needs.

Response to comments

Question: Can you arrange paternity leave/cover?

Answer: I'm asking Human Resources about the paternity leave policy.
Both of these courses are course which I developed,
so none of my colleagues in the department can teach them well
without investing a significant amount of time.
So I don't think I can find a colleague in my department to cover the course.

Yes, I would say that at the beginning of the course. In my case that was received positively, and when the day came they were very flexible in handling any schedule changes (much more so than students normally are).

I would also discuss this early on with your collegues. In my case they were very willing to help out (people are much less irreplacable as we like to think we are...)

This is definately something to discuss with HR, as there may be all kinds of policies and programs that you never heard of and could really help you balance your new family life with your work (as a colleage told me: however you will measure it, your life will change significantly (We both teach statistics), and he was right)


How to handle not being credited for research software development in papers? I worked for a publicly funded body. Whilst there I designed and developed a number of epidemiological surveillance applications.

I have left the organisation but since then I have noticed that some of my ex-coworkers have started to publish papers based on the data collected by the systems that I designed without crediting myself in the publication (in at least two cases directly referring to my system in the paper).

Since the publications wouldn't be possible without the systems I developed would I have any remit to ask for credit and/or authorship? How is this viewed any different from a co-worker using someone's lab results without credit for their own publication?

As per the comments on your question, I think this is really context specific and the role of an author can vary quite subtly from area to area. I'll try give a general answer to the general question first, and then look at the specfics of your case afterwards.

  How to handle not being credited for research software development in papers?

The first question is whether or not you should be credited for the software you developed in the paper. The answer is predicated on what precisely the contribution of the paper is and what the contribution of the software is.

If, for example, (part of) the core contribution of the paper is describing optimisations and techniques that you invented and applied in the software, then I think it is more than fair that you should be credited as a co-author.

If, for example, the core contribution relates to a methodology for doing X where your software was specifically designed for that methodology, then you should probably be credited as a co-author or, at the very least, mentioned in the acknowledgements.

If the core contribution of the paper is not directly related to the software itself but the software is used to some ends, then you should probably not be credited on the paper (otherwise Linus Torvalds would have millions of publications). But if the software system was described in another paper and played a significant/specialised role in the current paper, you could expect a citation.

  Since the publications wouldn't be possible without the systems I developed would I have any remit to ask for credit and/or authorship?

I think your reasoning is a little flawed here. Making a research paper possible does not entitle you to co-authorship (as a simple counter-example, if paper A builds upon the results of paper B such that paper A would not be possible without paper B, the authors of paper B should not expect co-authorship on paper A). Providing part of the core contribution of the paper—the reason why it was accepted in the first place—entitles you to co-authorship.

I noticed something crucial in your comments that you didn't clarify in your question:

  "Since xxxx our system has collated data on x cases and found that.."

The authors should absolutely not be claiming credit for a system they did not design or build. This is clearly wrong. (And it also indirectly suggests that part of the contribution is indeed the system and the authors are trying to claim credit for it.)

Since you know the authors, you should talk with them, show them the relevant quotes in the papers and tell them that you are not happy with them claiming the system as their own. Tell them that if they wish to continue claiming the system in future then you should be a co-author on the paper.

If you wish to escalate, you can contact the editor(s) of the journal(s) involved and tell them your story. The editor(s) might agree to let you publish a letter referring to the specific paper and outlining your case. This should be considered the "nuclear" option.

EDIT: Not in answer to the question, but this quote in the transcript of Hamming's address "You and Your Research" (well worth a read for anyone in research) reminded me of this question:

  I also did a second thing. When I loaned what little programming power we had to help in the early days of computing, I said, "We are not getting the recognition for our programmers that they deserve. When you publish a paper you will thank that programmer or you aren't getting any more help from me. That programmer is going to be thanked by name; she's worked hard." I waited a couple of years. I then went through a year of BSTJ articles and counted what fraction thanked some programmer. I took it into the boss and said, "That's the central role computing is playing in Bell Labs; if the BSTJ is important, that's how important computing is." He had to give in.


Professor wrote to me saying he supports my fellowship application to the committee A professor I want to work with (at the university I applied to) informed that he is awaiting some funding news (for a project I had expressed interest in working with him on) and he also stated that he has highlighted my name to the fellowship committee.
Any idea what that means? Is that a positive development with regards to me getting an admit/fellowship?

It is positive certainly, but not definitive. It is just a progress report sent as a courtesy. He is being encouraging, but not making any commitments.

Of course, you need to go through the normal admissions process. This isn't a substitute for any formal procedures that are required. In US institutions admissions is handled by the university, not the individual professor. Funding may be under his control, however.


Is SPIE proceedings publication a real scientific publication? I have some SPIE proceedings publications. However, in a scientific context does proceedings publication count as a publication?

The SPIE proceedings volumes are generally fairly loosely peer-reviewed conference proceedings volumes.  The quality of the peer-reviewing can vary depending on the organizers of each particular conference.

People do cite papers from these volumes and they're indexed by some research databases including Scopus and Google Scholar, but not Thompson's Web of Science (at least not the last time I checked.)  Like any conference proceedings papers, you'll have to take some responsibility for deciding whether the material is good enough to be worth citing.

You haven't explained exactly what you mean by "count as a publication."  Here are several answers:

Will tenure and promotion committees consider these as publications?  Probably not at the same level as publications in top-tier peer-reviewed journals, but they probably will be considered as conference proceedings papers.
Can you submit a paper for journal publication after publishing it in an SPIE volume?  Probably not, unless the journal paper is significantly expanded.  Publication in one of these volumes typically would count as "prior publication."
Should you cite a paper from an SPIE conference proceedings volume?  Yes, if the paper has useful information.  Readers of your paper should generally be able to obtain these papers if they want to look into the references further.
Is the SPIE a predatory publisher?  I doubt that anyone would argue that it is a predatory publisher.


A research validity issue and a work around I am working for a company that wants me to do a research related to using some sort of a technology. The research (which is going to be published) requires me to use a piece of a hardware which uses that technology. The company demands that I do all the analysis and the experiments to achieve the goal without mentioning the name of the hardware used which is an important part of the research.

Should I mention the hardware without referring to the name of the hardware?

I have used many resources related to that piece of hardware and I will not be able to mention them in the bibliography. Is this legal?

Does this affect the validity of the research?

What do researchers do in such a situation?

According to your experience is there a work around?

If you're going to publish a scientific paper, you need to give information on all of the significant methodology required to achieve the result.

It sounds like you are being asked to publish a paper that would be concealing vital information about its methods.  That may be legal, but it is clearly scientifically unethical, and reviewers in a quality venue would likely call you out on that failure.

If you're just doing the research for internal use (or informal publication, e.g., as a corporate technical whitepaper), then there is no expectation of methods disclosure, and there is no ethical barrier to being as vague as you like about your methodology.


As a referee, what should I do if I think the other reviewer of a paper is not objective? I was recently asked to referee a paper for a "moderate" but perfectly acceptable Elsevier journal, with an impact factor of around 1. The article in question was very poorly written, had several significant misconceptions in the introduction, but looked potentially quite interesting: I submitted a recommendation of major revisions, and included a list of fifty points ranging from the essentially (mathematical) grammatical to several significant scientific points. Frankly, I felt I was, if anything, quite generous -- rather than submitting a 2500 word review with a large number of salient criticisms, I would probably have been justified in recommendation rejection on the grounds that it was difficult to discern what had actually been undertaken.

Recently, Elsevier made me aware that the other reviewer had submitted their comments on the paper. I was interested to see if they had agreed with my judgement -- and on which side of the accept/reject fence they had fallen. Much to my surprise, they had suggested outright acceptance, had written a very terse review which included details that were not originally in the paper, but could only be known to one of the authors [or their friends].

What should I do about this? I feel like having a badly-written one paragraph review recommending acceptance of a flawed article makes a whole mockery of the whole of peer review -- and additionally potentially means that Elsevier can't select reviewers appropriately.

My perspective as an Elsevier editor: This happens sometimes and is easy to see through. An outright "accept" on a first submission is so rare as to raise eyebrows in any case (at least, in my field). The editor has probably noticed the lack of thorough review by this referee and will give the review the appropriate weight (i.e. none). That said, I would not see any harm in emailing the editor if you are concerned, so long as you keep it polite and to the point.


How do theorists in STEM fields update equipment? As a theorist my chief capital costs are software and computers (for large calculations and simulations). If starting at a new institution I would ask for these in my start up budget (about 20k USD). But in 5 years these items might all be obsolete and incompatible. What do I do then?

I understand that most schools have computer replacement programs every x years but the type of computers I would be asking for in start-up are quite expensive and not your typical campus machine.

I am curious what other theorists have done. Especially interested in those that might be at a primarily undergraduate institution.

I'm not at an undergraduate institution, but I am a theorist in a department that doesn't have many of them.

My summation of my startup costs were "People and computers".

A couple of things to potentially consider:

People. Support for a programmer, or a grad student, or undergraduate salary for the summer.
Consider negotiating for a recurring or longer term startup package. For example, my startup doesn't expire. I know someone else at another university who negotiated for "A workstation costing $X,XXX, replaced every 5 years".
Data costs. If you use data sets, or could conceive of using data sets that cost money, you want to allocate startup to those.
Similarly, travel and publication costs.

Another approach is to ask your Chair if the Department needs something, and put that in your startup in exchange for...favors, or unallocated funding, etc.


How does a standalone honours degree work? I'm currently trying to apply for a PhD position, but am unable to meet the entry requirements. My (potential) supervisor has advised me to undertake an honours year to meet the requirements.

I completed my bachelors degree in 2010 at a completely different university and everybody I've known has done their honours year as a part of their undergraduate degree before graduation.

My degree was titled "Bachelors of Computer and Mathematical Sciences" and shortened to BCM. So I would be

  Mr. LegoStormtrooper BCM

while my friends who have completed their honours would be

  Mr. Other Guy BCM(Hons)

For me, I can't just add on "Hons" because it would be in a different field at a different university.

So I am very confused about this. I've heard of Bachelors, Masters, Doctorates, Graduate Certificates, but never an "Honours degree" as an independent thing.

Can any one explain how this works?

I am familiar with the situation in NZ. Since Australia and NZ share many commonalities in higher education, i suspect that things are similar.

A normal bachelors degree is a three-year degree and by itself not sufficient for getting into a PhD program. An honours degree adds a fourth year to the bachelor degree and is normally open to very good students (there are GPA criteria for entry). In particular, an honours degree often involves a research project and is deemed sufficient for PhD admission. Most if not all people do the honours degree immediately after their bachelor. Generally, you need a four-years degree to get into the PhD, which can either be an honours or a master degree.


Grading schemes to encourage effort I'll be teaching a graduate-level mathematically oriented class with probably less than 20 students. I have to grade the students (our system doesn't allow for pass-fail grading), and while I don't want to be overly fussy about the grades (this is after all advanced level material and mostly Ph.D students), I would like to provide some incentive structure so students will do the classwork and hopefully learn something in the process.

One possibility is "coarse-resolution" grading where in each homework, the possible grades are +, 0, -, where + denotes having done about 75% or more of the work, 0 is between 50 and 75%, and - is below 50%.

At the end of the semester, the number of +/0/- determines the grade, with "mostly +" getting an A, "mostly 0" getting a B, and mostly - getting a C.

Is this likely to be effective ? Is there something else I should do ? I'm open to the idea of not grading at all and giving out dummy grades, but I do think that people who put in effort should be rewarded in some way.

One approach is to have a number of clear learning objectives. For example:

  At the end of this course the student will be able to differentiate functions of a single variable.

Then for each of these provide a description of what it means to obtain each of the various grades available.

  F: The student does not grasp anything about differentiation.
  D: The student is able to differentiate simple functions.
  C: The student is able to differentiate many functions, but has difficulty with composite functions.
  B: The student is able to differentiate most functions and employ the chain rule.
  A: The student is able to differentiate all functions and can apply first principles.
  A+: The student employs novel approaches to differentiation.

Of course, you'd need to tailor these to your course and make them more precise than mine.

The learning objectives and the descriptions of what each grade means can be given to the student. A course may have different learning objectives, each with their own description. Your assessment can be tailored to measure the learning objectives based on these criteria.

The idea, apart from making your job of assessing more objective, is to replace scores by learning objectives, so ultimately the course will not be about scoring points, but learning.
You could even disassociate the grades from the learning objectives and replace them by unsatisfactory, satisfactory, good, very good, excellent, and fantabulous.


Are there any actions professors can take online to contribute towards "service requirements"? I would like to fulfill my service requirements for the tenure review process.  My question: Is it possible to help fulfill these requirements through on-line activities?  E.g. Mentoring students online, or participating in some sort of on-line collaborative community?

@keshlam's comment is correct:  this is a question for the folks in your department. There are activities (internal and external) that feel like "service" that are not viewed as "service" ... it varies by department and school.  Just like expectations for research and teaching.

And make sure you ask folks who are giving you fact-based, not opinion-based answers.  You should have a tenured faculty mentor (if you don't, get one!), but they might not know the facts on this.  There should be an RPT chair in your department or school:  ask them.  You might also ask your chair:  if they chair views what you are doing as reasonable service, they may be able to argue for it counting, even if it's unusual.

But, in the end, this is not a question for anyone outside your school.  We don't vote. :)


What is the basic difference between a researcher in a corporation, and a university? What is the basic difference between being a researcher in a corporation, and being a researcher in a university?
Is there really any difference apart from giving lectures and grading student's exam papers?

As a researcher in a company, I need to take issue with the current answers as reflecting a very narrow view of corporate research. This view is common in academia and reflects the typically limited experience of university researchers with the diversity of the non-academic research ecosystem.
A large amount of research in corporations is, indeed, focused on the near-term needs of products. Companies whose business model is based on widget sales will tend to put their money into better widgets, after all. There are a lot of business models, however, that are not about widget sales.  Some examples:

Some corporations have government funded R&D as a long-term component of their business model. There are important aspects of the research space (even basic research!) that universities are often ill-suited to execute, including:

Research with high team complexity or high integration complexity (professors are not typically professional program managers)
Research that requires a high degree of quality control (grad students are often unreliable!)
Research involving classified or otherwise controlled information
Research at intermediate levels of maturity (where papers are scarce, but the relationship to widget sales is still hazy)

Some corporations have long-term strategic interests that they support by means of R&D investments, including university-like basic R&D. This was the old Bell Labs model (which is still going strong!) and it's still in play in many large corporations, such as IBM, Microsoft Research, etc.
Some corporations, especially non-profits, have missions that explicitly include research goals.
Some corporations are education-focused (just with different educational models), and carry out research as part of advancing their educational mission.
The boundaries between universities and companies can often become blurry, particularly around university "advanced ventures" organizations and in the medical space, where there's a near-fractal complexity in the academic/corporate relationships in many university medical complexes.

The life that you will lead as a researcher in these different sorts of organizations is very heterogeneous. Even within a single organization, such as the one that I work at, the goals and incentives are very different for researchers on the primary investigator track, the program manager track, and the implementer track. Even tenure can be less different than you might think, given the existence of fellows programs and the like.
So what is the basic difference?

All universities are primarily focused on student education, and all professor positions fall into one of a small number of career models.
Every other research organization is much less constrained in form, and you cannot make any assumptions until you understand their business model.


How important is advisor's supervision for a Ph.D. student to be an independent researcher? I have seen one extreme of the spectrum, where a person conducts great research without even attending college. For a student to become an independent researcher, how much is on the advisor's shoulder and how much on the student? I know the answers may be all over the map. Just curious what your takes are on this question. Anecdotes and personal examples are welcome.

I have noticed some professors are more successful in supervising students to become independent researchers (approximated by the number/ratio of alumni who land research jobs) than others, even though their research portfolios and student qualities are similar (e.g., in the same department). That's one reason I bring up this question.

There are two major types of advisor approaches which I've encountered during my studies:

Hands-off, abstract guidance only. Hint at which areas are interesting or currently active, but do not throw yourself into your student's work. Usually such advisors will gladly proofread the student's work for errors, but they rarely know what to do if a student gets seriously stuck. Advisor sessions may be spent discussing current trends, future work of either the advisor or the student or, in some cases, simply "life advice".
Co-worker approach. The advisor treats his student as an equal and tries to immerse himself into the student's work (or vice versa). By having a lot of exposure to the advisor's routine (how he goes around solving problems, how much time he spends doing research, how he prepares for lectures, etc.), the teacher aims to guide the student by example.

These two approaches are often seen in combination (while the student may be treated as a coworker, he still is usually the one to do the typesetting, the programming, and other time-consuming tasks).

Personally, I prefer the second approach, which is likely because I am not that settled in the "theoretical research" routine. Some of my friends, who have known since their Master's studies what they want to do, are very enthusiastic about having a well known professor with the hands-off approach.

To answer the question about either approach fostering independence, I believe the hands-off approach leads to much larger independence as a researcher, but the coworker approach may lead to a much better work ethic (mirroring the professor), which is tremendously important in science.

It seems to me that students have a harder time successfully completing research (asking the right question, having the right insights, etc.) than being independent. Therefore I believe that student/advisor relationship does not need to promote "independence" in any substantial way.


As a reviewer, should I act when the second reviewer did not seem to review the manuscript carefully? I reviewed a manuscript and suggested a major revision, which was done in meantime. Now that I receive the revised manuscript again, I see that the 2nd reviewer wrote only one sentence in his review to the first draft of the manuscript, although there were major issues at the theoretical, methodological, and linguistic levels. Should I tell the editor that I consider such a review insufficient?

I see that the 2nd reviewer wrote only one sentence in his review to
the first draft of the manuscript, although there were major issues at
the theoretical, methodological, and linguistic levels.

Are these issues not addressed in the revised submission (based on your comments)? Have the authors addressed all your comments carefully and satisfactorily?

Should I tell the editor that I consider such a review insufficient?

I would not do this. It is the job of the editor to see whether the reviewer has done justice to the article.

However, if you think there are still some issues with the revised manuscript, give it a fresh read and add more comments, e.g.
"I can see that the authors have addressed all of my previous comments. But, I still see that the article could be further improved if the following few points are addressed..."


Advice on publishing original theorems with easy proofs I got a rejection recently on a short paper that gave a fairly short proof that a conjecture of a well-known mathematician was false.  The reviewer said that “while the results are new and interesting,” “the proofs are fine, but not very difficult, and the techniques are not new.”  Nonetheless, the arguments previously evaded some top people in the field who were interested in the topic.  My question is, to what kinds of mathematics journals should one submit significant results whose proofs involve some clever trick rather than a revolutionary method?  Also, should one not strive to find the most transparent form of a mathematical argument?

There's a good chance the rejection is because your results are not interesting enough for the journal. In other words, the journal is looking for not only new and interesting results, but also complicated proofs and/or new techniques.
So: submit to another, probably less prestigious journal. Alternatively, you can submit to a similarly-ranked journal and hope the peer review process results in acceptance, which is entirely possible, because this particular reject reason is a judgement call and different people will come to different recommendations.


How to get lab resources back from a post-doc who resigned while on vacation and not coming back? I am posting this on behalf of my advisor.

A post-doc in my research group at US told that he'd be going home to meet his family who are in a different country, but after two months he emails that he is quitting. He has the laptop which my advisor paid for and important research data. He hasn't communicated in email that he will return the things he owes. Besides, he was playing tricks by procrastinating his return, even confirming his return tickets, only to finally resign.

What are the legal ways to get the resources as well as the monetary compensation made in his absence back, in case he doesn't respond?

(Note: The research data needs to be surrendered because it belongs to unpublished work from other groups, not because it wasn't backed up.)

The issues you are describing of misappropriation of university equipment, research data and unearned salary, rise to a level of seriousness that a rank and file faculty member is not equipped to deal with and will not typically be expected to deal with. It is time to call in the cavalry — by which I mean, the matter should be referred (probably through your advisor’s department chair) to the university legal counsel or similar office. They will take appropriate steps, starting with sending the absconding postdoc a threatening letter, and ending with who knows what (in theory, a police report and/or civil lawsuit, although given the negligible economic value of the misappropriated items and the difficulty of proving outright theft, I’m guessing not much legal action will come of the whole business).

Of course, I’m hoping that the postdoc will listen to reason and return what he has wrongfully taken, but in any case, if your advisor hands the matter over to the university authorities, and cooperates with the resulting follow-up actions, then even if the items are not returned, your advisor will be in a good position to explain to their funding agency and collaborators that they tried in good faith to fix the problem, and the embarrassment and damage to their professional relationships will be kept to a (probably negligible) minimum.

Good luck!


Is it OK to update code on repository after publication? Journals consider that is good practice to release script and codes to repeat the published results, and many of us I think agree with this practice. Code are typically deposited in software version control repositories (e.g., GitHub or BitBucket).

I wonder if updating the codes during reviewing process or after publications (which in my opinion is quite important, in general) remains a good practice.
Maybe the obvious answer is yes, but for example it is certainly not good to modify the data deposited for a published article (or modify its pre-print in a pre-print server).

Absolutely yes!  There is no reason to stop a project from evolving just because you've published about it.

What would be good to do, however, is to identify the version current at the time of publication with a release version or other similar sort of tag. You can point to the specific tag in the publication and also have the repository tag point to the publication through its associated comment text.

This will allow a reader to have the best of both worlds: access to both the most updated information and also to the precise version associated with the publication if they need it.


How to write my name and my job description in a publication? I'm a resident in a teaching hospital and not a staff member in a university, how to write my name and my job description in a publication as an author

Write your affiliation similar to how you'll do it with a university.

  First Last [Designation,] Dept., Institution

If your hospital does not split members into departments, then Dept. part can be omitted.

Examples:

Aaron Stone
Neurosurgeon, XYZ Clinic

Cathy Miller
Researcher, Cancer Research Lab, BCD Hospital

Greg Thompson
Cryogenics, GHI Health Institute

Note that it is not always necessary to include your designation (job description), unless the publisher asks for it.


Is a paper more likely to be accepted if one of the authors is an associate editor for the journal? I'm about to submit my first scholarly manuscript to the top journal in my field, which has an acceptance rate of 20-25%. One of the co-authors on my paper, besides being generally well-known in this field, happens to be on the editorial board of this journal as an associate editor. Obviously I imagine that he'll automatically be excluded from the review process due to conflict of interest, but does their affiliation with the journal increase the chance of the paper getting accepted?  I should note that the paper has already been through several rounds of internal revision and I've received excellent feedback so far from both this particular coauthor and others.

In principle, no.

In actuality? It likely does, under a couple of different mechanisms:

An editor might be slightly more likely to give your paper the "benefit of the doubt" if its a borderline case between Revise/Reject, etc. This may also be true if your co-authors are "known" names, regardless of their editorial position.
An AE at a journal likely has extensive experience writing for, and reviewing, papers in that journal. As such, they probably have a good sense what kind of papers they're looking for, the tone they should be written in, etc.

So the answer, in a practical sense, is likely "Yes, but not by a huge amount." And possibly not after controlling for recognition and experience.


A master's degree from IGNOU is eligible for a CSIR -NET qualification? If someone completes his master degree in mathematics from Indira Gandhi National Open University (IGNOU). Can he be eligible for a CSIR -NET application?

CSIR -NET is a necessary qualification for lectureship or junior research fellowship in india given by the Council of Scientific & Industrial Research (CSIR).

The requirements for the NET application can be found in the CSIR homepage. Take a look into the main notification documentation.


Is it possible to trade up during ones PhD in Mathematics? I have been accepted into a Ph.D. program at a school that is a decent top 50 on the US News. Has anyone had any experience with 'trading up' after one gets their terminal master? At my undergrad, there have been cases of students entering the Ph.D. program and then transferring after 2 years to a better institution after getting their terminal master. Would this be a feasible plan?

For example https://mathematicsgre.com/viewtopic.php?f=1&t=836&p=4603&hilit=trade+up#p4603

Yes, it is a feasible plan. But it's not straightforward.

Things to keep in mind:

the PhD advisor in the first school might have different expectations. One might consider being open about the plan to get only a Masters's degree. Otherwise, it is both unfair to the advisor and can lead to many issues.
to get to a different PhD program, one will need good letters of recommendation. Thus, the relationships with your original PhD advisor are important.
expected prolonged graduation times: residency requirements, different courses schedule, and in general B.Sc. + Ph.D. usually (!) are faster than B.Sc.+M.Sc.+Ph.D, especially when different levels are completed in different educational institutions.
you might get better or worse financially but getting qualified or disqualified for some scholarships. This is strongly dependent on the individual factors and exact policies of educational institutions.
change (drastic/slight) of the research topic, which can be also a good thing or bad depending on the individual factors.
in case the PhD application to a new program fails, one might have already burned some bridges, and certainly did not help themselves in the pursuit of a PhD.


Choosing a title for a research paper What are the best practices for writing a research paper title? I am looking for some general guidelines.

Does one go with short and sweet?
Or a bit longer and informative?
Should one phrase it as a question or rather as a statement?
Should one use humour and play on words?
What should one avoid?
Are titles written different for different areas of research? (i.e. Computer Science, Maths, Neuroscience etc.)

Follow the conventions of your target journal or conference. The most reliable predictor of how a title will be perceived is if other papers at the same venue have had similar titles.

Specifically, your question Are titles written different for different areas of research? can be answered with a clear yes. For example, compare the following programming languages and neuro-imaging venues.


How to write an introduction for a conference or journal paper efficiently? When writing research paper, I am often stuck and spend a lot of time working on the introduction. Most of my time spent is staring at a blank page... The introduction takes me significantly longer to write than any other part of a paper.
How can I speed up the writing process for the introduction? I feel that once I can get a reasonable draft that I can iterate quickly, but if I just write nonsense, iterating isn't that useful.
My field is computer science/engineering.

Write it last.
I'm in CSE too. I always start my papers at Section 3: Methodology. Then I write subsequent sections, only interrupting to fill out bits of Section 2: Related Work whenever it becomes apparent that I need extra contextualization. I carry on until the Experimental Results section is complete.
At that stage, if time permits, I like to let the paper lie for a few days, and get busy with other tasks. On the backburner of my brain, ideas will form on how to frame the paper. That framing is represented in the paper by the trio of Abstract, Introduction, and Conclusions. Of these, I've found that it works best for me to write the Conclusions first (iterating over the main message of the paper, and how that message is evidenced by concrete results from Tables and Figures), and then write the Introduction such that it matches the Conclusion. Finish it off with the Abstract.
This is my process, and you mileage may vary, of course. But I've learned that if you write the Introduction of the paper first, it takes forever and the result will not be very good. You most likely need to change the Introduction anyway once you have written your Conclusions. So keep it for last.


Is there a way to register now for the GREs, or attend grad. school some other way? I have my Bachelor's and want to go to grad. school—and I want to go as soon as possible. I recently quit my industry job (I hated it) and am now searching for a job at a university. I can't register for the GREs now, it's after the deadline, but there are some other options I've thought of:

Take classes in a Master's program, take the GREs in April and try to get into a Ph.D program
Apply to universities that don't require the GREs (some in the US, but most in other countries)
Find a way to register for the GREs

My degrees are in, and my target field of study is either Physics or Mathematics. Do you folks have any suggestions, or judgments regarding the viability of my above presented options?

(P.S. - This question is not off topic. Any single person who did not register for the GREs, but still wants to begin grad. school could use this question. Nothing depends on "personal preferences" because my personal preferences [outside of wanting to begin grad. school ASAP] are in no way relevant. The answer accepted is appropriate, and easily generalized.)

I recommend you go for a Masters degree first. Some schools admit Masters students without GRE. While doing your masters, you can prepare for GRE and take courses that would eventually count for your prospective PhD degree which you are intending for. This will benefit you getting into a good PhD school which otherwise may be very difficult to get in.


Advantages of second marking In the UK a portion, and in some cases all, work is "second marked" where an independent marker also marks the work. In cases where the 1st and 2nd marker disagree, a 3rd marker may be used. Finally, the entire work of each student over the course of his/her studies is evaluated by an exam board with (sometimes) 2 additional independent markers. These exam board markers tend to only consider cases that are on the border of different degree classifications.

From my understanding of statistics, having all of these different markers will regress marks towards the mean. As I am currently faced with the daunting task of 2nd marking a large stack of off topic papers, I am curious what are the advantages of second marking?

Double marking has many roles, but mostly it is to ensure accuracy and fairness. The main way of achieving this, and avoiding the statistical anomalies alluded to in the comments is to produce an effective marking scheme, so that academics with sufficient background can grade the exam and produce virtually the same grades. Easier said than done.

More details can be found on the Internet, for example, on Swansea University's website.


How ethical is the practice of including spouses as co-authors when they are in the same field? I've noticed many situations where a researcher will put their spouses as co-authors in a paper. This is commonly seen in situations where both spouses are in the same field. Valid collaboration between spouses is possible (and exist).

The question is not meant to attack spousal collaborations in academia. Simply put, this is just one possible example where a conflict of interest might arise (the same question can be placed in situations of parent-child and parent-sibling collaborations with no significant difference).

However, where does one draw the line in such a situation? What is stopping them from putting each other in every paper they write, effectively "doubling" their academic output? Whether we like it or not, publication metrics are used in fellowships, grants, awards, and many other situations in academia. In order for it to remain an objective metric requires the integrity of authorship to be upheld. When a PI is choosing authorship, they are responsible for not only themselves, but those in their own group, as well as their department and institution.

The situation with spouses (and other familial relationships) is somewhat unique in that the barrier for co-author contribution is far more easily passed, compared to two regular collaborating PIs. Not only are they often more readily available for collaborations, there is also a possibility of subconscious bias when evaluating the contributions of a significant other. There is also a greater possibility such a system can be gamed. For example, could such a possibility arise where a contribution which would otherwise be recognized in an acknowledgement be replaced by co-authorship due to a slight bias?

The issue is not whether or not spouses, family members or any other person should be allowed to be a co-author when they have made a valid contribution. The problem lies in whether or not the judgement of valid contribution can be made fairly without a conflict of interest by someone in that situation. Being aware of this, is it ethical to still make that decision? Is there a way to be unbiased without complete recusal?

Your question is based on one assumption (that you spell out):  "the barrier for co-author contribution is far more easily passed [for spouses], compared to two regular collaborating PIs.".

"Yeah, well, you know, that’s just, like, your opinion, man." -- The Dude

As pointed out in a comment, ethical people don't draw the line in different places depending on the situation (at least for the case in question). The line is already drawn by the ethics principles they follow.

So, to answer your question, it is ethical to include spouses when the spouses contributed to the paper, it is not when they didn't. Exactly like including anyone else.


Should article submissions be formatted in draft format, or in the format of a particular journal? Some journals do not require article submissions to be in any particular format. Would it still be better to try and copy that journals usual format, or use a generic draft format? Would you as an editor or a reviewer prefer one over the other?

For example, many articles use a two column format that is nice and compact for publication, but is a little harder to review and markup - so maybe the reviewers would prefer the article in a single column draft format?

EDIT: I'm specifically asking about journals that state you can use any format you like (for submission), leaving you free to choose whatever will be most convenient for the editors and reviewers. Do you try and still present a "finished product", i.e. format it like it will be if published - or use larger spacing, etc. to make it convenient for review. What would you as a reviewer or editor prefer in the absence of set submission guidelines. Or would you not care in the slightest?

Depends from journal to journal.
There are journals like Decision Support System that require from author to use specific format for initial submission, which btw differs a lot from format of their online publications. It seems to me that format specified in their Guides for Author is designed to ease review process i.e. making side notes and underlining by hand on printed copy.

There are ones like Information Processing and Management, that clearly state they are following "Your Paper Your Way" policy, which in essence: allows you to use any citation style and format for initial submission.

And there are journals, like International Journal of Cooperative Information Systems, that make no such statement, but if you read carefully instructions for authors - they say: that you'll have to apply their template / style / format after being informed on acceptance of your manuscript.

So, unfortunately, there is no easy answer. It would make a lot of sense if all journals follow "Your Paper Your Way" policy, but it is not the case. Many times, you are left in uncertainty due lack of explicit instruction on this.


Do editors know how many papers I am refereeing on the same platform? I have very recently returned two referee reports for two different Elsevier journals. Within two days, I have received two new requests from the exact same two journals (but from different editors).

Of course this might be a coincidence, but now naturally I am wondering: did these editors somehow know that I had just 'freed myself' from the previous commitments and was again available as a reviewer? Is there, for instance, a field in Elsevier's online platform that tells editors how many assignments I have at a given time?

I think there are two aspects to your question:

1) Do editors see how many other papers you are currently reviewing?

Yes, in fact this feature is supported by at least some submission systems. I am not sure about Elsevier, but below is a screenshot from Manuscript Central (also known as ScholarOne):

The second and third column list how many open reviews the person has, and when (s)he last submitted a review.

2) Do editors care? Are you more likely to get new reviews when you have submitted your current ones?

In general, they will likely not care too much. At least in CS there are myriads of different systems in use, and knowing that a person has currently no open reviews in any given one of them tells me close to nothing about what her or his total review backlog looks like. Further, it is not my place as an editor to decide whether the person can take on another review - I can invite her or him, and they will just decide for themselves. That's what the Accept / Refuse buttons are for, after all.


Advantages/disadvantages of bundling source code from separate, related papers? Say that you have several papers, each with a set of experiments, in which the source code overlaps appreciably. If you wish to release the code for each paper, which is better:

isolate the relevant code and release each (possibly redundant) version independently; or
keep the code bundled with clear instructions of how to reproduce the experiments from each paper (say by indicating which revision number corresponds to the code used in each paper)?

This scenario can arise, say, because each paper includes the same benchmark algorithms or the code was initially developed to be extensible (with, e.g., good memory management). It may be faster to deploy new code by extending the existing code base. One can imagine a public github repository where the software suite is continually expanded.

Some advantages for isolating the code:

Easier to understand in the context of the single paper
Clearly reproducible

Some advantages for bundling the code:

Greater visibility for all the papers
More likely that software from older papers is up-to-date and easy to run
Builds towards a comprehensive software suite
Less redundancy and less overhead (assuming this is the manner in which the code is developed)

  Is there clearly a preferable choice among these alternatives? Is there another alternative entirely? Have I enumerated the most important advantages in deciding between these alternatives?

I face a similar situation. I'll tell you what I'm planning to do, although I don't claim this is the best approach. I think it's a reasonable compromise between making things easy for the reader, and making things easy for me.

First, I wrote several libraries that I keep on GitHub. One or more of these is needed to reproduce the research I'll discuss in each paper. I'll create a release for each library, with a citable DOI using Zenodo. A set of instructions is available.

Likewise, I'll have a configuration file, plus some scripts, and maybe some data, that are unique to each experiment. This is where I'll put the README file describing how to build/run everything. I'll create a GitHub repo for those as well, and create a release using Zenodo.

So each paper I write will cite all the library/other releases needed to reproduce the software.

EDIT: One advantage of this is that while the DOI will point to the exact version of everything I used for my published results, it will also be clear where people can go for the latest version of everything.


I'm required to apply to multiple projects but I'm interested in only one I'm interested in applying to a Ph.D. position and the guidelines indicate that a given number of different projects (of a range of open positions) should be indicated. I'm interested in one in specific and the other options fall completely outside of my interest or even my specialty. This is required because a potential interview will include members of all the chosen projects, what approach is recommended for completing the list?

You will always have to work with more than one faculty member as a PhD student. Certainly during your class work, you must be prepared to interact with other faculty. During your research, you will figuratively (and perhaps literally) have to "go down the hall" and talk with another faculty on a topic that impacts your research because your advisor is not the expert on that part of the work. Finally, your dissertation committee will contain more than one faculty member.

The reason you are asked to select more than one faculty at this point is to give you the opportunity to prepare for the above situations well enough in advance. We have another reason too. Suppose that I am a faculty member who is to interview a potential PhD student for my research group. I would be far more impressed to hear the student tell me that he/she already knows about my colleagues that have potentially useful contributions to make than I will be to hear the student say "No, I had no idea that person was here".

Take the time now to get to know the place where you plan to start your life-long career. Learn to network by learning how to get to know who to contact to start your networks.

This exercise in discovery carries over ten times or more when you are later going to interview for a faculty position at a university. Do you believe the department where you will apply will be impressed when you know only about that one person in the department who has the research equipment that you need for your studies?


How to find double blind peer review journals in physics? I have tried googling but couldn't get a definitive answer.
Could anyone suggest/list Journals that allow a double blind peer review for physics, preferably, particle physics.

Why is "double blind" your principal concern?

There are many sites that will list major journals by discipline and sub-discipline.

Here is a listing of Physics journals with bibliometric data http://www.scimagojr.com/journalrank.php?area=3100

Once you've found relevant journals, just read the journal website to find out how they do peer review.

However, normally the "double-blind" aspect would be a minor consideration relative to other criteria for choosing a journal, such as impact, relevance of manuscript to journal, and quality. In other cases, you may be able to request double blind review if you are particularly concerned about that aspect.


Decision time on a postdoc offer while applying for other positions I have recently applied for several postdoctoral positions as well as a lecturing position. A week ago I had an interview for one of the postdoctoral positions and I should know the outcome of this interview by the end of next week. During the interview I was asked if I was applying for other positions, to which I said yes and briefly described what these were.

The project is a very interesting one but I also want to consider the other positions I applied for (especially the lecturing one) if I were to be the preferred candidate. However, I will have to wait until the end of February or so to hear about these other positions.

So, if I was chosen for this postdoc I was interviewed for, I was wondering how long it is acceptable/customary to make them wait until I give them a final response.

I'm sure they would be ok with a couple of weeks, 1. because moving overseas can be a bit of a change from a personal perspective and 2. because considering other potentially interesting opportunities makes sense at this stage in my career, but I was wondering if making them wait for a month or so was too long.That being said, I heard about people making an employer wait four months or so but I would find it rather impolite.

Thanks for your input!

Most likely, you won't be able to "make" them wait at all.  If they give you an offer, they will also give you a deadline to decide whether to accept it.  You can ask for an extension of this deadline, but there are no guarantees that they will agree to extend it.  The power here is mostly on their side, not yours, unless you are really a superstar, or are the one and only qualified candidate.

For a position like a postdoc, the employer typically has a fixed number of positions available (often just one).  Commonly (especially for a field with an academic-year hiring cycle) they interview a number of people and then make offers made serially.  Every day that they wait for you to make a decision is a day in which the next person on their list might take another job, reducing their options if you turn them down.  So it's not in their interest to give you an indefinite amount of time to decide, since that could result in them hiring someone not as good, or not being able to fill the position at all.  They don't want to rush you into declining, but they also can't wait forever.

It's hard to predict what kind of deadline they might give you.  Some employers will give a candidate a very short deadline (a few days) if the candidate is a "reach" - the employer doubts that the candidate will accept, but wants to at least try to get them.  This way, in the likely case that the candidate says no, not much time has been lost.  More commonly, the deadline would be on the order of a week or two.  Having as much time as a month seems unlikely, but there are a lot of factors that could affect it, and if they are not tied to the academic year there may be more flexibility.

What "makes sense" to you from a personal perspective (pondering an overseas move, exploring options, etc) is not really the employer's concern.  Even before receiving the offer, it would be a good idea to carefully consider all the pros and cons, and come to a tentative decision about whether you would take the job if offered (including scenarios about other offers received or not received).  Between the interview and your own research into the institution, you should have almost all the information you're going to get; the only extra information in the offer itself would be the salary (and other benefits).  So ideally, as soon as you get the offer, you should know how you intend to decide, or what other offers you need to wait for.

It's entirely possible that you may have to make a decision on this position before hearing about the others.  That's just how it goes.


Why data falsification / fabrication is found after degree is awarded? I saw on the internet that many degrees are revoked due to data falsification, but the question here is: how come colleges cant identify data falsification or manipulation before the degree is awarded? Do colleges have to wait for another person to report the misconduct and waste time and money?

There are two things to consider, in my mind, when thinking about your question.

The first is the possibility for sampling bias. If someone is caught falsifying data prior to their degree being awarded, they are likely expelled - and it's unlikely for the work to ever see the light of day. These detections are largely "silent", while the flashier ones that involve clawing back degrees, retracting papers, etc. are likely over-represented.

The other issue is to consider how data fabrication is detected. On a crude level, it's a function of both time and the number of people looking at the work. Inherently there's more time post-graduation than pre-graduation. There's also a larger number of people looking at it, especially if the work is being published. So if the detection of any given fraudulent work has a fairly low probability per person interacting with the work, it's entirely reasonable that the majority of these cases would arise after a degree is awarded.


Which one is more valuable in a postdoc application? a full paper in a B* conference or a short paper in a A* one? Assume the hiring committee (Computer science) are reviewing the CVs of two Ph.D. graduate's with almost equal skills/expertise.

Regarding their best publications, one has 1-2 short papers (e.g. 6 pages) in A* conferences (top-tier) whereas the other one has 1-2 full papers in B* conferences (second-tier) in comparison, and both of them have an equal amount of other publications in lower ranked venues and journals.

Then which one can have better chances in getting hired as a post-doc researcher?
Consider

A short paper at an A+ conference is better on your CV than a full paper at a B+ conference, because readers will pay attention to venues and will most likely ignore paper lengths (even if you include them -- which you probably won't, because they take up room).

But, it seems like you're trying to decide upon a venue on the basis of only the immediate impact on your CV, you should take a broader, longer-term perspective.

Backstory: The OP's paper was originally ten pages and it has been accepted at the A+ conference on the condition that it is reduced to six pages.


Should I inform my bosses that I'm about to start doing a PhD research? I was recently admitted in a PhD program, I haven't started any research yet and Intended to keep my full day job and try do a research while working.

I think my bosses are unaware of this for now but the thing is that I would like to brag about me doing a PhD by posting on Facebook and LinkedIn.

Doing a research will probably put some additional pressure on me and from a certain moment on, I will probably have some duties at the University which might obligate me to spend some time on campus. That will affect to some degree when I'm able to work an probably my performance.

Would it be safe for me to post and update profiles on Social and Professional Networks and do I need to officially inform my bosses first?

PS. My Job is something of a embedded programmer and the future research will be about image analysis and pattern recognition. I think the job I do and the research are not directly related but after all there are embedded devices running vision algorithms. I also think that my boss could agree to a more flexible working time.

Of course you should!

Certain duties such as a committee meeting would require you to ask for a leave permission from your company. If you break it then, you'd be in trouble. In certain institutions, it is mandatory to provide an NoC (no objection certificate) from your company as part of the PhD admission process. You should've done it before, but the earlier you inform him, the better.


If you have two bachelor's degree in related fields, can you mention in your CV only the latest of the two? I obtained my bachelor's degree from a third tier school before completing my second bachelor's degree and a master's degree at more reputable schools. I was wondering if it is acceptable to omit my first bachelor's degree from my CV.

I think it would make for an awkward line of questioning at an interview when they inevitably ask what you did during those years and you reply that you completed a Bachelors degree but didn't feel it was good enough to include it.

Worst case scenario: your interviewer went to that institution and you've just shot yourself in the foot.

Always include your full educational and work experience as it makes for easy nitpicking at an interview that is easily avoided.


What is the optimal balance of time spent on research vs. volunteering/leadership/organizing in grad school and beyond? In graduate school I have found that along with being a producer of good research, fellowships/post-doctoral advisers/faculty search committee are also often interested in what one has done outside of research (or teaching/TA-ing) as well. Examples of such activities include (but are not limited to) volunteering with younger students in science, organizing a journal club, mentoring undergraduate researchers, etc. In some cases, the importance of these activities is immense: for the NSF CAREER award, for example, having outreach is a substantial part of the application.

However, clearly, spending all of one's time on these activities is not the best idea, since then no research gets done.

So, my question is:

What is the optimal fraction/amount of time to spend on "outreach" activities like those mentioned above, which are explicitly not research or teaching activities, for someone looking to pursue a career at a research university?

Short answer: You should spend "some" time on volunteering and leadership activities.

Unlike an undergraduate student, a graduate student is primarily focused on research, so you don't want to spend "a lot" of time elswhere. Even so, proficiency in other activities is something of a "tiebreaker" against another candidate with comparable research activities that doesn't have "outside" activities.

This is in contrast to undergraduate work, where "leadership" is the "whole game" for some students (for later life)--provided they pass their courses.


dissertation cover photo I am going to submit my doctoral thesis, one of the optional things we can do in our university is having a photo of author on the back cover of hard copy of thesis. I have no idea for that. How do you think about that?

It is very likely that nobody except you and the people you will give your thesis to will ever see the hard copy of your thesis. (And some random people looking at some theses in the library - however, if this is not uncommon in your university, they will not judge you negatively for having a picture.)

So, you should consider:

Do you think it's nice to have a photo of you on your thesis? Many people like to have a nice thesis on their shelf which has not only good context, but nice formatting, nice colours, nice pictures etc. Some people see a thesis as a pure formality and are happy to do as little "style" things as possible. In which class do you fall? And if you care, do you think the thesis looks better or worse with your picture?
Will the people you give the thesis to appreciate it? (Don't forget to consider parents and grandparents!)
How much more does it cost? Do you feel it is worth the price?
Is there a place at university you really like (e.g. a certain place in the library, your office, the mensa etc.) and you would really miss it after your studies? It can be nice to have a picture of yourself in that place on the thesis (if this is allowed).


What is a diplomatic way to tell a professor that progress hasn't been made because of their lack of communication? Here is the scenario: in a collaborative effort, our group was to work with another group/professor to write a paper on some work we had previously done. I, a grad student, am to be the main author/architect of the paper. But, and this was said explicitly by him and my own professor, I was to write it with lots of help from the collaborating professor, and under his guidance and direction.

In other words, I would talk to him, get direction like "you should focus on this topic for the paper" or "don't pursue this, it won't be interesting to reviewers", and I would do the actual work/research/writing.

However, since making this agreement, months ago, he has gone basically incommunicado. I'll send him an email and not get a reply for literally a month. I've asked to set up a short (<1hr) meeting, at basically any time of his choosing, and just no response. Several times, too.

Let me be clear about this too: I'm not really that upset about the lack of communication itself (though, I'll say this single thing about that: when he is actually in person with me, he is constantly checking/answering his email on his phone, so I know he does do it, just apparently not with me). I'm not dying to write the paper, it's not a cutting edge thing that will get scooped, and I have several other projects. It's a little annoying in general that he has been flaky, but I'm plenty busy with other stuff, so again that's not too bad.

Here's what my question is about. I both suspect, and from my short interactions with him I've had in the past few months, that he is going to ask to see what work I've done on it since he became uncommunicative, to which the answer is "minimal". The reason is that I am busy with other projects, and because he wasn't doing his part of this, I didn't know which direction to take. I could certainly speculate and choose one, but that is very risky (timewise) for me: if I spend several weeks pursuing something and it turns out he doesn't think it's a good fit for the paper, welp, I just wasted several weeks. And that has happened to some extent.

Because it seems like I wasn't clear about this initially, I'll say it explicitly here: my goal is not to attack him, or bring this up. If he seems fine with the (lack of) progress made, then I'm very happy to leave it be and just continue on. But I strongly suspect (and he seemed to say) that he expects me to have done more. For this question, assume that the professor will ask why more hasn't been done on the paper, so the subject will come up.

So, how do you say this tactfully? You can't really respond with "because you were uncommunicative, I didn't get very much done, because it very possibly could have been for naught", because that's pretty accusatory and will ultimately not help solve the problem.

Is there a good way to say this?

What is a diplomatic way to tell a professor that progress hasn't been made because of their lack of communication?

You don't.

That is, I don't think that would be very productive, diplomatic or not. I wouldn't focus on their lack of communication in the next meeting you have with them at all; I would instead focus on using that next meeting you have with the professor to come to some resolution on the things that are delaying progress on the paper/project.

As you mentioned in the comments:

  I essentially have done everything I can, within reason. I've selected and done background on directions for the paper.

So, this is what you have, and this is what you show them. Additionally, any questions about the scope/direction of the paper, etc. should also be brought up during the face-to-face meeting.

To address additional information posted by OP:

  But I strongly suspect (and he seemed to say) that he expects me to have done more. For this question, assume that the professor will ask why more hasn't been done on the paper, so the subject will come up.

We all have limitations. You were in charge of certain aspects of the paper/project, but you were not able to achieve a certain level of progress that was set. Just be upfront about that. Specifically, tell the professor what it is you are stuck on and ask them during your face-to-face meeting if they have any feedback to offer.


Appropriate to meet with prof. to discuss low quality exam I am in an MBA program and last week had a two part test for a marketing class. I was under the impression the first part was just analysis, essentially creating models and writing notes on trends so you can quickly and easily answer the questions on the test (take home, given 3 hours to complete during the regularly scheduled class time).

The first part was much more extensive and actually had 6 questions with 3 sub questions per question to answer and I would've liked to have spent 12-15 hours on it versus the 8 I allotted myself. Because of my poor planning, I produced incomplete work and the completed work was NOT up the quality I usually produce and expect of myself. I did email my professor to ask for a possible extension and explain my situation. He would take off 25% for turning it in the next day, I did not take this option as I felt I could do better than that turning it in by 11 pm that night.

I am embarrassed and humbled. My professor is a very nice guy and a great teacher.

Would it be appropriate to schedule a time to meet with him to discuss the quality of my exam and how I would have approached it differently?

I am not looking for brownie points or extra credit or anything of the like. I just can't stop thinking about how I would have approached some of the questions differently. My ego took a hit and I'm essentially looking for redemption in a way.

Yes. If you would like to discuss the exam, schedule a meeting and talk with your professor about it. It seems that you have already discovered the core issues impacting your performance here - a lack of sufficient planning and the resulting lack of time - so it may be helpful to consider what you hope to learn from such a meeting. Are you hoping your professor knows some way to accomplish more work in less time? Are you looking for some confirmation that you really couldn't have done better? Your professor may have useful feedback but will likely agree with your assessments about planning.