I am in the final stages of a M.Sc. in bioinformatics and am currently writing my thesis. While I was writing I noticed that one of the datasets I used for a major part of my project is quite problematic and may have somewhat biased the results (if it matters, the data is from a published paper. A postdoc working with me an the project have reviewed the paper and suggested that it would be appropriate for our work). I do not think this is very major bias, and I can give a concrete explanation as to the source of this bias, but still I bias.

I am considering of referring to all of this in my thesis as part of a broader discussion of the limitations of my work.

Knowing my thesis supervisor I suspect that his reaction will be something along the lines of “why did you use this dataset in the first place? You should have looked at the data before using it.” In retrospect I wouldn’t have used this dataset and yes, I should have looked at the data more carefully. However, at the time I was doing this I had no prior experience with this type of analysis, and therefore did not know what types of problems to watch out for (I was also put under continuous pressure from supervisor to produce results, which did not give me much time to ensure the quality of the data, but this is a different problem).

From my perspective, learning to identify and avoid such problems is a valuable part of my learning process, and I therefore consider it important to demonstrate this learning process in my thesis, but I don’t think my supervisor will be appreciative of this, and I really fear backlash from his. To make things more complicated, we are currently writing a paper based on these results and I fear my supervisor will blame me for undermining the paper by using this dataset.

My questions therefore are:

  1. Is it at all appropriate to use a master’s thesis to demonstrate my learning process in such a way?

  2. How do I balance between my desire to be honest and show what I have learned and between the harsh response I am likely to get?

Thanks in advance.

I would like to download a database containing all scientific papers published. This is obviously too broad and ambitious. To be realistic, say I want all the papers searchable on google scholar (although other databases are fine, say SemanticScholar, etc.), or an approximation of that. What databases out there allow you to download this data?

I don’t want to download the papers themselves (that wouldn’t fit on my storage), just a record containing title, authors, journal (if it is not a book), year, and perhaps abstract.

Is this possible? How can I download a database like this, that I can browse and search offline?

I have recently received reviews for a journal paper I submitted a few months back. The verdict is a major revision (three out of four reviewers requested this, the fourth said accept with minor revisions).

Many of the reviewers felt like we did not justify our approach sufficiently, to which we agree and can improve upon. The editor; however, in their comments to us, stated that we should take a different (much more complicated) approach altogether (even though none of the reviewers suggested changing the entire approach, only to justify why we chose the approach we did).

Question: How should we proceed when the editor’s comments seem much stronger than those of the reviewers?

It is not feasible to accommodate the editor’s requests by the deadline. I’m unsure if the reviewers made (stronger) private comments to the editor requesting larger changes or if the editor interpreted the reviewers comments much differently than we did. The paper will go back to the reviewers after we make the requested changes.

This question is aimed almost entirely at “higher” education faculty, regardless of the branch(es) of knowledge that they represent.

My intention is not to be rude and/or to insult people here, jut to give some of my thoughts about an assignment of homeworks and/or similar tasks.

I did some research in the field of “assigning homeworks and/or similar tasks”, mostly by talking via my facebook chat with students and people who finished their college and who are from Croatia, and, when they had some courses in which there was an assignment of homeworks or similar tasks, some instructors(professors) insisted that the homework must be solved and given to them, while some were not so strict and for them the student had either the possibility of giving her/his (or his/her) homeworks so to obtain extra points which could affect their final grade in that course.

If you ask me, both of these methods of work are not good enough, the first one is extremely destructive, and the second one is destructive (but not extremely), and what is being destroyed is relationship professor-students and, also, the motivation and inspiration for the course itself.

Because, the professor should do precisely this:

1) She/He should do all that he can to motivate and inspire as much as possible as many students as possible in such a way that they do see that the course that they are attending is interesting and worthy of research, and is probably needed later in such a way that other courses will be built by some (or all) knowledge that comes from the course she/he is giving to the students.

2) She/He should explain to students that it should be good for them to try to solve some exercises in the books they encounter, and she/he could give to them some exercises that could help them to gain better understanding of what is going on in the subject-matter of the course, because even if some youngsters are determined to do very good research work and/or to teach, or to do one of those two things, they will probably do it better if they actually were solving some exercises and problems and saw from that how generalizations are and can be obtained, and how an attitude toward doing some exercises can raise questions that can clarify a lot what exactly is going on.

3) She/He should explain to students that the test(s) they will have to write (or, more generally, attend to) will include in itself the obvious requirement that they were not lazy during the duration of that course, and that they will have a better chance of passing the exam if they decided to practice (during the course) various approaches and methods in their adventure of solving some exercises and, more generally, tasks, and the more they exercise in a right way the more they will master the subject-matter of the course.

The approach where students must do a homework, or where they need not to do it, but if they do not do it then their grade can be lowered down, or be not as high as it could be if they did the homeworks are non-inspirational and contain in itself an elements of force (I could also say violence, but will not), because, some gratitude should be shown to those youngsters, because they actually came to listen to you, and want to learn something new, and want that you inspire them, and want that you be good to them, and want that they have as much freedom as they can during the attendance of your course and during an activites that are related to your course.

And what do you do? You put on their shoulders a burden of “necessary” homework or of “not needed but I could reward you if you do it” homework.

But, they can work in groups and/or with themselves only, even if they are not forced or “almost-forced” to do something. They will surely do exercises if they are interesting to them and if they are presented to them in an interesting and clever way.

Yes, there will be some that will not do them them even with almost the nicest and cleverest approach presented to them, or they will do them but will not feel the need to present them to someone, be it professors or colleagues attending the same course. And there will be some that will gladly do them and ask professors for better approach and/or advices. But neither group will not feel less worthy because some did the homework and succeeded in attaining the higher grade, and some did not and because of that their grade is lower than of some colleague who did all or almost all of the homework assignments.

So, I am just thinking of an approach where everything will be at least as good as it is, but where there is no tendency to reward in this or that way students who wanna do their homework and exercises in the course, and not to reward those who do not wanna.

I should tell that English is not my native and I am not good at it, so it could be that I did not reflect my thoughts crystally clear the way I wanted.

So, it would be nice to know what do you think about the concept of studying where there are no homeworks and/or similar tasks that must be done, and of the same concept where are also no homeworks and/or similar tasks where doing them could award some students, and not doing them could not-reward some other students?

Also, as I am not a professor anywhere, it could be that I am not competent for even asking something like this, or to go into discussion about approaches of this kind, and also, all of this was researched only with students or those who finished the college in Croatia, so that I do not know generally what is the situation in the whole world.

I’m an undergraduate in computer science. I will complete my undergraduate course next year. I’m really interested in mathematics especially applied topology which recently saw great uses cases in neuroscience, material science and quantum computing.

Would a PhD in mathematics allow me to work on these fields later? ( AI, Physics, Neuroscience, Quantum Computing ) or is it wiser to go for a PhD in Neuroscience or PhD in Computer Science?

If I go with mathematics, which areas of it should I concentrate more to work on neuroscience and quantum computing?

The question is really an attempt to ask for help and advice from academic staff members, industrial research staff or anyone who has had personal experience with Post-doc job applications.

Obviously there are lots of websites that list post-doc positions, and some are dedicated just for that. However in reality these positions have a lot of hidden intricacies that might lead you down a path that has been a dead end for a long time. The applicant however learns about this just at the very end of the process.

This is somewhat frustrating since most of the people I know about looking for a postdoc are in the final stages of their PhD and really cannot afford to waste too much time on the wrong thing.

Some ideas that raise my concern into the straightforwardness of a postdoc application are:

  • Many Post-Doc positions are advertised just for the sake of advertising the position, however sometimes the successful candidate had been chosen already, even before the position was open !
  • A lot of advise I get is that i should contact the concerned Professor/person directly and not wait for a position to be open, being proactive
  • Some positions are just out of reach for fresh PhD graduates because other previous post-docs are also applying for the same position and so the competition becomes unfair

I am hoping that this question leads into real world, clear and effective advice for people looking to get a Post-doc position

I am looking to acquire resources in the name of indigenous Western Saharan refugees or citizen. If I were to engage a kickstartererer for this cause how would you advice.

I am thinking mainly solar powered ocean centric medium; considering the noise and pollution in the general area, do you not think the local wildlife could go with some vehicle frequency reducing traffic:?:. Main functioning concepts; gamification | general mathematics | non-competitive comparison | low-resource impact; 3 year estimate

This question already has an answer here:

The core of the problem is already in the title but I feel as i should add some more details.

I was doing some mathematics and, if there are no logical flaws or mistakes of any other nature (it seems that there are none) I managed to prove some result that, again, if it is proved with no errors, would, I believe, enrich the field in which it belongs.

Of course, I immediately started to think about arXiv.org and I decided that I want to submit an article there, but, when I was reading help section, there stands this, written:

Note: It is a violation of our policies to misrepresent your identity or institutional affiliation. Claimed affiliation should be current in the conventional sense: e.g., physical presence, funding, e-mail address, mention on institutional web pages, etc. Misrepresentation of identity or affiliation, for any reason, is possible grounds for immediate and permanent suspension.

But, as you are aware by now, I do not belong to any institution and as such, am not affiliated with any, I am just an amateur that among all fields thinks about mathematics the most. So, I have stumbled upon this cautious note quoted above and do not know what to do.

So, I decided to write to all of you here to see what can be done in this case of mine. I am not 100% sure that among all sites this is the one most suited for this problem of mine (for example, I could have written this on MO Meta or MSE Meta) but surely I will try to welcome opinions and help, even if they do not resolve this issue that I am faced with.

What should be done?

EDIT: This is not a complete duplicate of the question mentioned in such a way as this one is a duplicate of that one because the body of the question mentioned goes like this:

“Assume you have already completed your undergrad and have been working for a number of years. Does one need to be part of a university or a learning institution to publish papers?”

But, I did not complete my undergrad and I am working for a number of years (independently). so, there are some similiarites but the question is not exactly the same, although answers seem to fit well.