text:
Should my references be famous if I want to get into top schools for PhD?
So I've been researching my field of interest and I'm increasingly getting drawn to apply to a few "top" departments (in pure math) -- it seems like such a strong fit at the moment given that I've done relatively serious undergraduate research, though it was more of a "directed" study kind of thing, and my approaches to some of the problems have been fruitless, but have gotten me exposed to so much mathematics that got me excited to learn and think more about the topics I was looking at initially. I have the grades and the GRE scores (past the 80th percentile on the subject test in math, which seems like the unadvertised minimum). However, my reference letter writers don't appear to have any connections to some of these top places. From some research online, it appears that admission committees want to hear from known mathematicians -- but what if my reference letter writers aren't known in said department? Is such an application doomed from the
start?
For people who have served on admission committees, what is your take on this and how would you advise an applicant like me? Unfortunately there's no time to rectify this by going to an REU or the like.

There is always time to rectify by doing a Masters first.

@Artem - Your comment seems to imply that such a reference is required, is that what you intended?

It's not necessary for your recommenders to be famous.  It certainly helps a little, since it's only natural for the admissions committee to be influenced by fame, but it's not really relevant to the quality of the recommendation so most people try not to be too influenced by it.  Instead, these criteria are more important:

Do your recommenders know you?  I.e., can they make detailed, substantive comments, beyond just listing grades?
Do they know what's required for success at the schools you are applying to, and what the competition is like?  Do they have a good basis for comparison in your case?  The best case scenario is if their students regularly apply and are at least sometimes accepted; then a comparison with past students is very informative.
Does the committee understand their personalities and writing styles?  Some recommenders are very optimistic and say everyone's great, while others lean towards understatement.  If members of the committee have read previous letters by your recommenders, or know them personally, then it's much easier to make a reliable judgment.  Otherwise, everyone will be at least a little more skeptical of the letters.

There are plenty of people who satisfy these criteria but wouldn't register as "famous" in the community at large.  On the other hand, if your recommenders don't satisfy them, then it will be harder to be admitted to a top department.  I wouldn't go so far as to say it's impossible, but this is worth keeping in mind when selecting letter writers.


text:
From whom do I get references when my original advisor leaves academia?
This is similar to a previously asked question, but deals specifically with addressing the problem on the CV. My adviser had a bit of a personal meltdown and left the department while I was finishing analysis of field data/writing up. His students were assigned the following year to a non-tenured professor.  This new professor was of little help to me my last year of writing up, sat on my dissertation with no comments for over 6 months and only produced comments after I went to the departmental chair. He did not think much of the type work I was doing and went so far as to say so during my defense. I will add here that I have a number of publications (>5) including single authored ones-which for my field is significant- as well as an excellent track record of funding and in presenting my research. I have a strong CV but have had no success thus far in securing a job. I once saw one of the letters he had written for me (it needed to be included in a single PDF so he had to send it to me) and it was terrible. It talked mostly about him and how he really did not know me well and with a few generic sounding "he will no doubt exceed" sentences that just sounded fake. Months later a colleague suggested that I find a different reference than my adviser (but was not clear as to why).
So, my question is this: since committees will no doubt look at my list of referees and wonder at my lack of an adviser-I have taken to including a short "note" in the "reference contact information" section explaining that 1) my original adviser left academia at the end of my time as a student and 2) that my new adviser was up for tenure the year I defended and very busy and was in a different field than mine, so instead "below are three people who are in a better position to judge me on my research, teaching, writing skills".
Is this providing too much information or is this instead ensuring that rather than questioning and then rejecting my application the committees will stop and think "oh okay, I can see why the applicant did not include their adviser"?

This is a sufficiently different question that I've changed the title to reflect the different aim and prevent closing votes, but otherwise I've left things the same.

Related: http://academia.stackexchange.com/questions/635/how-to-handle-not-having-my-phd-advisor-as-a-reference

Is there a problem if he leaves academia or if he leaves Academia.StackExchange.com? ^_^

Ask other people on your PhD committee.

Your current advisor's letters are killing you.  Do not ask him for any more letters.  Do not list him as a reference in your CV.  Don't walk; run.

I will add here that I have a number of publications (>5) including single authored ones-which for my field is significant- as well as an excellent track record of funding and in presenting my research.

In that case, you really should have no trouble finding enough other good references to overcome any concerns raised by not having a letter from either of your advisors.  Everyone reads advisor letters with a grain of salt anyway; strong letters from well-known senior researchers outside your home department have much bigger impact.
Of course, if anyone asks why your current advisor isn't writing you letters, you should answer honestly, but I think adding an explanatory note in advance is unnecessarily defensive.

I think a statement that the current advisor was administratively assigned and does not activel supervise the sudent's research is not overly defensive, and has the advantage of being true. (if this is not explicitly stated in a letter, it should at least be made clear in the CV.)

You should definitely get rid of the letter from your new "advisor."  I think it would be reasonable to list only your original advisor as your advisor on your CV (not the new advisor).
I think you should make sure that one of your letter writers includes a short paragraph explaining that your advisor left academia and this is why you do not have a letter from your advisor.  I would look into whether there's someone you can ask for a letter who feels some responsibility for your original advisor, for example, your advisor's advisor or a frequent coauthor of your advisor.

+1 for asking another letter writer to explain the situation.

Assuming your field is relatively small, the odds are good that your advisor's fate is known to the community. Unfortunately, such events do happen, for all kinds of reasons—just a few weeks ago I learned that a relatively prominent academic in my field basically had his group wiped out because he was arrested on some rather nasty charges!
While it doesn't seem that your original advisor befell such an awful fate, it is clear that, for whatever reason, he is no longer in academia. However, given that he is probably known to many of the people working in your field, it might still be helpful to try to get a letter from him, even if he's doing something completely different. If you can't, because he has refused to do so, then you are entitled to explain the situation in your CV or cover letter. Be succinct and to the point, and stick to the facts; do not make it into a "sob story," which will not endear you to a hiring committee or postdoc advisor.
And good luck—such situations are always stressful, and are always unfortunate for the students caught up in them. It's one of the pitfalls of academic life, and I don't know of a good way to deal with it.

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text:
Do you write "letter of recommendation" on recommendation letter?
Almost all examples I can find in the internet do not say "letter of recommendation", however there are a few which do.

It doesn't matter.

Why do they say not to? That sounds inane.

It’s frustrating to have to look for a bunch of emails titled “Letter of Reference” to find the one about a particular student or post doc candidate. Alternatively, if I’m on an online platform, I want to make sure I’m reading the right letter.
So, as a matter of convenience for anyone handling the letter, I include a header

Letter of Recommendation for Anna Goodresearcher

or something similar as the subject of my letter. That way, it’s immediately obvious who the letter is for, making life easier for whoever is organizing or evaluating the applications. If it’s a postdoctoral reference or something else being sent directly to an individual by email, I try to include this in the email header as well.

And those emails with the subject "My CV"...

Don't see why not, or why you should avoid it.
I really hate it when people stand on ceremony, and seem to be more worried about the format of something than the substance. No offense, but I don't think it matters, if anybody will read that letter of recommendation they'll be skimming through it.

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text:
To what extent do Easychair Scores Affect Acceptance/Rejection in Theoretical Computer Science Conferences?
My coauthors and I have submitted a paper for a well respected conference in a subfield of theoretical computer science. This is the kind of conference where the authors receive feedback before the final decision, and they have a chance to respond.
Some information:

There were about 240 submissions. I know this because my paper was sent in the very last minutes and the submission server closed precisely at the announced deadline.
The conference accepts between 25-30% of papers. In the last year there were about 80 accepted papers for about the same number of submissions.
Each reviewer of a paper gives a score from the scale -2(strong reject), -1(weak reject), 0(boderline), 1(weak accept),2(strong accept).
Each reviewer gives a confidence score to its review. I think that it varies from 1(not very sure) to 5(expert)
Each paper has three reviews (ideally).

Once, when talking with a colleague that uses to participate on program committees he told me that in many conferences, a great percentual of papers are accepted/rejected only with basis on the score given by easychair, while those that are not so clear go to voting.
Questions:

What percentual of papers are usually accepted automatically, i.e. only with basis on the automatic ranking system of easychair?
Which score a paper should receive to be a clear accept? (assuming the paper has no flaws, and that no program committee member will claim to have found a flaw.)
My paper got a score of (2,1,1), that is to say, one strong accept and two weak accepts. The reviewers confidence were not disclosed but from the reviews I could see that they were either 4 (high) or 5 (expert). Would such a score guarantee the paper to be on the safe side?

especially in TCS it's very hard to say. I had a submission with score (3,1,1) which was rejected, and another with (2,-1,-2) which was accepted (in different venues)! (The -2 was not because of any flaw, just profound disagreement on the model used). BTW many conferences have [-3,+3] range.

Scores alone are meaningless. Suppose you get two accepts and one reject because one reviewer found a flaw in your result/proof/model/related work and the others missed it. Then you will probably be rejected despite having a good total score. Or the PC may read the reviews and decide that the strong scores are not justified (e.g. the reviewer didn't read it properly) or vice versa.

I've served on the program committees of several major theoretical computer science conferences, most recently SODA 2017.

What percent of papers are usually accepted automatically, i.e. only with basis on the automatic ranking system of easychair?

Negligible.
For every submission, the assigned reviewers are asked to come to an agreement whether to accept or reject.  Each submission is assigned a shephard to guide the discussion and summarize it for the authors.  For the very few (≤5) submissions that receive only strong-accept scores, this discussion is usually perfunctory ("This appears to be a clear accept; any objections?" "Nope."), but not always.  The discussion is based on the content of the reviews, not just the scores (which may have come from subreviewers, who can't calibrate against other submissions).
For most conferences, the number of papers with supportive reviews is larger than the number of papers that can be accepted.  Especially later in the decision process, PC members are often asked to rank remaining papers, including papers that they were not assigned to review.  That instigates a higher-level discussion about this paper versus that one, or this AREA versus that one, which is rarely reported back to the authors (because the other submissions are none of their business).
In short: A paper with strong reviews can still be rejected because a majority of the other PC members preferred something else.

Which score a paper should receive to be a clear accept? (assuming the paper has no flaws, and that no program committee member will claim to have found a flaw.)

There is no such score.
I have seen submissions with scores of (2,2,1) rejected after discussion.  Typically for such papers, PC members are encouraged to reduce their scores to reflect the discussion, but that does not always happen.  I don't remember if I've ever seen a (2,2,2) submission being rejected after discussion, but that doesn't mean it can't happen.

My paper got a score of (2,1,1), that is to say, one strong accept and two weak accepts. The reviewers confidence were not disclosed but from the reviews I could see that they were either 4 (high) or 5 (expert). Would such a score guarantee the paper to be on the safe side?

Definitely not.  Most papers with those scores are accepted, but definitely not all.  Certainly I've had several conference rejections with similar scores.
More broadly: There is no "safe side".

what does it mean PC members are encouraged to reduce their scores to reflect the discussion? Do PC members reduce the scores given by sub-reviewers to better justify rejection? Does the opposite hold?

When the initial reviews have wide variance, PC members sre encouraged to discuss the discrepancies and then edit iews and scores. For example, if a PC member initially rates a paper very highly, but another review points out a major bug, the first PC member might lower their score. Conversely, if one PC memebr thinks the problem is unimportant and initially gives a low score, enthusiasm from another reviewer might convince them to raise their score.

Also, technically, the final score always comes from the PC member, not the sub-reviewer. If the PC member thinks the sub-reviewer is too generous, they might lower the subreviewer's score; if they think the sub-reviewer is too harsh, they might raise the sub-reviewer's score.

That is very interesting. Then why the reviews sent to the authors have "Reviewers Confidence and Score" if they correspond to the PC member, even technically as you say? What's the point of the sub-reviewers if PC can change score and reviews at will?
I think I will post it as a new Question because I had a rather (as I thought at that time) bizarre situation with the PC of a conference for which I was sub-reviewing.

The point of sub-reviewers is to save PC members' time.  PC members don't change reviews "at will", but in response to information unavailable to the sub-reviewer, in full view of other PC members. (EasyChair shows the complete revision history of every review.) Don't assume bad faith.

Thanks! I never implied bad faith, on the contrary. I was just not aware that PC members are allowed to touch/change the review/score.


text:
Showing book cover in public presentation
I have a follow up question from my previous question that I thought could be of benefit to others if they had the same question.
I’m giving a public talk for a sci-com event and wanted to show some books that people could read if they were very keen and wanted to learn more.
Is there a copyright problem if I just showed the cover of these books in the presentation? I’d imagine it’s the same as looking at a book at a bookstore, but I could be wrong (has happened before!).
Would I need to at least acknowledge the authors and publishers?

No, I can't imagine anyone objecting to free advertising. It is just a visible citation, actually. If you think the people at your talk will want to follow up, you could also provide a list of titles and ISBN numbers to make it easy for people to acquire the books.
Whether your presentation could be considered a "republication" of the graphics or not, I can't say. Not a lawyer here. But publishers in general would be happy to have their wares pushed like that. If you were putting those graphics into some (printed or online) publication, you would possibly need permission, but the titles etc would be enough for such purpose anyway.
In any case, in the US, at least, showing the cover or even snippets from the books is probably covered under fair use if this is an academic use. In particular, you aren't reducing the value of the work by showing its cover.

True, nor am I getting any profits from it. It’s not an academic talk in the least, it’s to laypeople outside of science and my discipline, so folks would have to be suuuuper keen.

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text:
Addressing a poor student-advisor relationship in job interview
I have a couple of interviews for research assistant vacancies in the next few days, but I didn't list the advisors of my undergraduate research project as my references, even though I added the project details and listed them as the advisors. I left them out of the references as the relationship I had with them wasn't that great. It was solely a case of a poor fit between a student and advisors; they had a particular way of providing feedback and comments that worked really well for some students but didn't work for a lot of students. I unfortunately fell into the latter camp.
I want to emphasize that they were not bad people, but simply because the fit, both professionally and personally, was probably quite poor to begin with. They've had students before that really blossomed under their supervision style, but it required a particular kind of student with solid coping mechanisms that I unfortunately did not cultivate at the time. They've also had much more personable relationships with other students as well, one which I did not have with them; we only talked about the thesis. Again, it wasn't their fault, and I can't emphasize that enough, but it was just a case of a really bad fit that I unfortunately did not see at the time.
With interviews for research assistant positions coming up, I'm not sure how to address this if it's asked. For example, 'Why weren't your advisors listed as reference?' or 'How was you're relationship with your advisors?'
Worse still, 'Would you be able to provide us with the contact details of your undergrad advisors?'
Has anyone else been in such a position before? Have you had a relationship that made you not want to list your advisors as a reference? Has it come up in interviews before, and if so, how did you address it?
If you're a PI for a lab, what would your initial thoughts be on this? Are all poor advisor-student relationships a red flag, or do you consider each circumstance on a case-by-case basis?

What part of the world are you in? "Interviewing for research assistant positions" is not really a thing in the US...

@cag51 Good observation, as you may have guessed, this is outside of the US. It's a Commonwealth country, or at least one of the countries that were formally/still part of the UK colonies. Sorry for being vague, I tried to keep this anonymous for myself and advisors in question. I hoped that the circumstance could be applicable to many different people who may be faced with the same problems.

Try to focus on the positive in interviews (well, and life :-). Explain why you recommended whoever you did recommend. Say that you thought the people you recommended could give the best assessment of what you would be like on this particular job, and why you thought they would be good at that. Point out (if pressed) that your supervisors are listed on your CV and could of course be contacted, it just wouldn't be your own first choice.

I really like that you kinda hit the nail on the head with an overarching principle that can get me through the entire interview (and possibly life, indeed!) and some pointers that stayed parallel to that important principle. I already feel better about the interview!

The advisor-student relationship is only of higher importance in such an interview, when the student has to and is still learning a lot and needs regular supervision and guidance. It comes down to division of labour in the end, how much supervision and control an advisor wants and invests of his time on the student and how much supervision the student needs and wants.
So you could argue that you are a very autonomous person, self-teaching new material to yourself etc... Of course, it's a bonus if you can also connect easily with all types of persons and cultures and did so in past and are able to make compromises. But it would be rashly to exclude you from a job position (in my opinion), because you seem like a difficult personality, as this phenomenon is not uncommon among some of the historical renown and very successful scientists, mostly because such had very personal ways to think and conduct their work with the will (not inability) to not make compromises. Just don't overweigh this issue. Other questions, criterions and answers in an interview are much more important and personally I would prefer a difficult but autonomous and creative person over someone who needs constant and unbroken supervision.

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Are there a specific form when a co-author withdraws from a study?
There are 3 authors in a research paper. One of the co-authors wishes to withdraw from the study. Are there any forms that need to filled up? A form stating that the co-author has no say or hold or ang whatsoever to the paper anymore. He/she would literally give up all his/her rights to the paper.

Are you asking about a publication? About sponsored research? This is unclear.

Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.

An ongoing research paper. It hasn’t been published yet. Unfortunately, one of the author wants to withdraw. Is there any form that he can fill up or complete stating that he will have no right with the paper if ever it gets published?

Normally the answer would be no. A letter from them stating their withdrawal would be sufficient. However, it is possible that there is some interaction with a funding agency where they are already named and the agency requires notification.
It complicates the work, of course, since their intellectual contribution to date needs to be properly acknowledged. It may require rewriting any paper(s) to cite their work. Otherwise plagiarism issues might arise.


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When is it OK to list publications from a previous institution
I've published a few articles on some work I did at a previous research institute. I've recently moved to a new research institute and have continued much of the same work. The new institute wants to put up a list of publications to demonstrate the skills and expertise of their current staff there and would like to link to some of my old publications, without altering anything in them.
Now I can surely see the value in showcasing "this is what our people can do" and I don't see any harm in it since it will still clearly show the institute where the work was originally done, and is inline with the current institutions work, but it might be seen as padding an unfair attributions.
Is this a matter of opinion or are there clear guidelines here?

In my experience, employers/institutions vary in their policy whether they prefer to list "work that was done here" or "work/experise our employees have" - which is both fine. So I'd say it's more a matter of your employer's opinion.

I'm not sure whether I understand the question correctly. What does it mean to "put up a list of publications"? What precisely is going to happen with that list?

Always.  If you wrote it, you should list it.  The list of publications associated with each member of the staff explains what they bring to the organization. Collectively, it gives a picture of the talent they've assembled.   But anyone reading these lists has to know people move around and that if, for example, you had a best paper in your previous position, it's still a best paper and of course you'll list it -- and that you'll list any other publications as well.  They'll expect you to list them all.
I think most people will take for granted that some of your publications probably happened elsewhere.  If they click the link to read your paper and it recites your differing association at the time, they will know for sure that it did.


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How can the summaries and statements linked to particular references be identified?
Although there are plenty of search engines which allow you to identify citation links - paper Y cites paper X - are there any which identify what statements and summaries are attributed to paper X? You type in the DOI for paper X, and in addition to a list of which papers cite X, the list of particular sentences in each of these papers which refer to X are also received, e.g.

"The world is round" [paper 1]
"The curvature of the world has long been debated" [paper 2]
"Both Flat Earth alternate theories have been proposed as to the shape of the world" [paper 3]
"It is widely assumed that the world is round" [paper 4]
etc etc.

If a citation search tool like this exists, can it also be used to link from declarative statements, to references cited in support in that statement?
For example, Statement == "The world is round" - 215 hits, of which:

139 unsupported by citations
24 supported by reference X
12 supported by reference Y

and so on.
Do any academic search engines with these capabilities already exist?

If I didn't correct the title properly, please do a rollback.

I pretty sure this does not exist.  It would require a level of sophisticated text parsing that has not been developed by computers.  After all, not all statements that the earth is round are going to phrased the same way, and for such a tool to be useful, it would be necessary to identify statements with the same semantic meanings.  This is not possible with the current language processing techniques; it would be huge advance if a computer could reliably parse and identify logically equivalent statements.  So you are not going to find what you are looking for.

Thanks. I don't think this would be a very tough text parsing challenge though: look for a text string in a series of texts, then look for particular combinations of symbols (e.g. [x], (1), something superscripted, a non-standard word followed by a four digit number, perhaps with 'et al' in the middle), then look for something that corresponds with this series of documents at the end of the text block.

The hard part is not picking out references, it is identifying the claim that the reference is being used to support (or whatever).

It doesn't need to be anything as complex as you described. All it has to do is to automatically index the sentence in which the reference was made, and maybe the sentences before and after as well. Computers can do that very easily; they don't need to understand any meaning--they only need to be able to identify the reference. It's up to the researcher to decide if that context is useful or not. That said, I agree with you that even something on this simpler level probably doesn't exist, not yet anyway.

Thanks both for your comments. I'd have thought that, given we've got self-driving cars and Quiz-willing AIs, something like this should be with us already. The two main uses I could think are: 1) to identify whether something you've written has been interpreted in the way you intended, or whether it's become shorthand for stating something you didn't intend it to; 2) (more contentiously) to quickly identify a way to cite something, where in the field it's become an expectation that it should be cited, in such a way that it's unlikely to be contested.


text:
Repeat citation for consecutive sentences
When the next sentence in the paper or thesis shares the same citation with the previous one. Should cite one time only at the end of the 2end sentence or cite 2 times - one for each.
For example:
In the following paragraph, 2 sentences follow each other share same citation. Should I remove the 1st citation or not.

Hybrid ... registration method. (Mani and Arivazhagan 2013) Combine
  the output of intensity method or f... method will be the input of another.
  (Mani and Arivazhagan 2013)

Maybe add page numbers to indicate that you cite different parts of the same work?

Another solution is to replace the first formal reference by an informal one: Mani and Arivazhagan demonstrated that ... and then put the formal reference at the end of the whole passage based on their work.

Similar to @greenb, maybe write: "Mani and Arivazhagan (2013) blah. They also blah-blah." Starting the second sentence with "they" makes it clear that you are referring to Mani and Arivazhagan. Similarly, you could write "their method", "this technique", ...

I've heard that in fields different from mine this is referenced with (Ibid.) for footnote-style citations. I am not sure about inline citations, but the Chicago manual of style says it is ok. If you google for "ibid references" you get more hints how to use this.

I would recommend asking your subject-matter librarian. They are usually very familiar with the various citation methods used within your field and would be able to provide advice. Or, they'd know where to look for a potential answer.


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What is an "author's novelty file" in journals?
Recently I submitted a paper in a journal then after a few days I got following comments:
Your submission of the manuscript  has been unsubmitted. This is because your "Author's Novelty File" was not detailed enough. In order to proceed, please briefly describe, in a few lines, the new contributions of your paper to the field. Do not repeat for this purpose the content of your abstract. Instead, provide a brief itemized list of these contributions in a separate file.
I don't understand what I have to write now. What he is asking for? I need help with this.
Thanks for giving me time.

@CharlesMorisset yes sir  http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0207

It sounds like the journal wants you to identify in what manner your paper has expanded the state of knowledge in your field. Have you contributed a new experimental method? Or perhaps you've provided new insights into some sort of phenomenon, or measured data for a new material, or so on. These contributions should be collected in this "novelty file."

I recently submitted a paper to IJNME. In the 'File Upload' section, it states the following:

"Author's Novelty File" - All Authors are now required to supply an additional
      file. Please briefly describe, in a bullet pointed list, the new contributions
      of your paper to the field. Do not repeat for this purpose the content of your
      abstract. Instead, provide a brief itemized list of these contributions in a
      separate file.

I hope this helps.

I think they're asking for an "explanation for non-experts".  Often, the abstract of a paper gives only enough information to be fully understood by an expert in the field (or at least in that problem).  Part of your job in explaining your work is explaining why it's important.  Think about how you would explain your work to a student with roughly the same background as you, but who hasn't thought much about your project.  Now think about how you would explain it to a researcher working in a completely different field... in 5 sentences or less.  Your novelty file should say something like that.  Emphasize here's what we added.

This doesn't seem to be the point of this exercise. This is, I think, a screening tool for the editors to see if a paper is worth forwarding on to reviewers at all.

@aeismail What criteria do you think they use to decide whether to forward it to reviewers?  It seems to me that it would be based heavily on "Why is this important?" and "What did we add?"  Otherwise, wouldn't the abstract suffice?

Some journals may have stances against "incremental papers"; a paper that basically corrects or slightly improves on the work of others may not be as eagerly sought as a paper that presents something that is mostly or entirely new.


text:
How to ensure a research idea has not been explored previously
I am admittedly an undergraduate so I do not have very much experience yet in finding resources.
When I have an idea of something I would consider worthwhile to research (in my case for a proposal to a supervisor about an undergraduate research opportunity), assuming I do extensive research online to see what has been found out about the subject and end up concluding that what I want to look into has not been investigated yet.
How can I ensure that it actually hasn't, and it isn't just a case of me not finding the information that is already available somewhere?

You can ask on some of the SEs: those that might be relevant to you are bio.SE and cogsci.SE.

That is part of "extensive research online" of course ;)

It's almost impossible to know for sure that a result is new.  As suggested in the answers, ask experts and read the literature (a citation index is helpful).  In spite of this, at least 3 times before I've worked hard on a result, only to discover it was previously proved, usually a decade or more earlier.  Don't feel bad.  This happens to most people.  When it happens to you, be thankful for what you've learned in the process.  Often the experience will help you later on in unexpected ways.

This is of course always hard to protect oneself from. However, I would say the best way to ensure that your research proposal hasn't been investigated before is to get in contact with an expert in the field and ask him or her this.
Of course, you should investigate the topic thoroughly before approaching the expert. One tip to do this is by using a citation index. This enables you to track how a certain paper has been cited, meaning you can follow the trail and more effectevly find out what has been done. For example, if you have located an old seminal paper in your field, finding out which papers have referenced this one should give you a fair chanse of finding what you're looking for.

As an undergraduate doing research, your primary goal is to learn and publishing is secondary. Of course, publishing your results and going through all the associated things for the first time is part of the learning. There is nothing fundamentally wrong with spending your undergraduate years rediscovering something. To bring up a particularly relevant example for today: Alan Turing was elected a fellow of King's College in 1935 (at the end of his undergrad) by proving the central limit theorem. He failed to notice that it was already proved in 1922. I am sure he learned a lot from it.
Of course, you have to be prepared to rediscover. If you are not it can be very discouraging. From a person experience, when I was an undergrad preparing my first first-author paper for submission I ended up finding previous work that had shown almost the same results 3 years prior. I had spent a lot of time rediscovering the ideas and writing my paper and it was a pretty devastating blow. My supervisor's words of encouragement: "Don't worry, at least we know we're on the right track".
He was right, and I was able to learn a lot from the experience (eventually leading to other publications). The particular paper in question sat in the back of my filesystem for a while, but I returned to it 2 years later with fresh eyes to discover that it was not as derivative as I had originally judged it and even this paper ended up being published (with some modifications) at a conference.
Another adviser takes the idea of rediscovery even further. When we move into new territory on a project, he will suggest some directions knowing that the relevant theorems have been proved already. He will tell me: "this result has been proven, but don't look it up, you will arrive at it on your own and then we will both be able to understand it better". This approach works very well in math-like fields since you have the advantage of knowing what you are going after as true, but still get to experience all the joy of (re-)discovery and the lessons you learn along the way. Something that is often not obvious from just reading somebody else's paper.
As an undergrad, don't worry about accidentally working on something that has been done. Concentrate on learning as much as you can!

My answer is probably hidden in the previous ones but I'll give it a go anyways:
1) never assume that you discovered a completely new field: if there's something that I learned in my research years is to be humble. Maybe soeone starts very boldly thinking that they're the best researchers in the world, but for sure everybody at some point realises that the field is populated by experts, who know a great deal of things in the area. So in the case of finding out others sharing your ideas, humbly try and learn from them; in the (exceptional) case of really finding out a new research avenue, humbly start collaborating with others because you won't make any difference to the field only working by yourself.
2) similar ideas do not prevent you from engaging on the same topic: this is very common, and I've seen it happening a lot of times. Researchers become depressed when they see that something similar to their ideas has been published already. I think that what happens there is that you find something related, and even if you did not do the work, tend to believe that you would have done exactly the same steps. It's only when you engage directly with the problem that you discover that you would tackle it (slightly or vastly) differently: that gives you a lot of potency in my opinion, and it's a very good exercise. Take an existing problem, which has been tackled already, and give it your spin.

"I think that what happens there is that you find something related, and even if you did not do the work, tend to believe that you would have done exactly the same steps." - it becomes really depressing when you realize you would have done exactly the same as what they did for their first step, before the other 9 steps that go a lot further than what you had even considered for now. And then, halfway through the paper, you discover they describe the result of those 10 steps as okay, but vastly inferior to their actual contribution ... ;)

Several years down the line, I'm now be able to answer this question myself: you can't exclude it, and this isn't limited to academic topics. People will disclose what research, products, startups or concepts they are working on at conferences, competitions, social events,... but you can never know whether they're working on something and intentionally not disclosing it. Internet research is the closest you can get, supplemented by asking people who know the field you're interested in.

Nowadays, people usually submit the preprints for the papers on arxiv. Hence, if you have an idea you can search the databases(arxiv and different research engines such as inspires in physics, for other topics I believe it would be different) by different combinations of words and see if someone else explored that particular idea. You shouldn't be bothered by the novelty of an idea. Suppose you have an idea and you work on it, the outcome would be in general very personal. Even if someone proved a known result and therefore can not publish this result since it has been published before, what one gained in the precess is more than just an idea. In the process of exploring an idea, one develops the techniques which are necessary of creating/observing/exploring ideas in the field, and in no time a new idea which hasn't been explored before comes in.
In the end, don't bother with this problems, just go ahead with the research.

"Nowadays, people usually submit the preprints for the papers on arxiv." - that is very field-dependent. In my HCI-related CS subfield, the concept of publishing preprints is rather unheard of, and the only times I usually hear about arXiv at all is here on Academia SE.


text:
Why is the date left out of some academic papers?
Being somewhat familiar with referencing of academic papers as a source, it has struck me as odd why authors would leave out some date on their paper. The date could be the day the author completed the paper on or submit date or published date etc.
Certainly it would be of help to others who would want to reference their work?
So, does anyone know if there is a specific reason why certain authors leave out a date on their papers?

Based on the answer here, maybe the question should be resubmitted as follows: "Why don't all academic papers include the 'submitted for publication' date?"

Welcome to Ac.sx! Your comment and reformulated question will probably not be seen by many here. I think it might be useful if you post it as a new (follow-up) question if you are up for it.

@raghu: The journal includes that information or not; it's not usually up to the author.

There is often a substantial delay between when the author finishes a paper and when the paper is actually published. The author may not be totally aware of the publishing date. This is why the authors do not include the date.
The date is generally found in/on the book/proceedings that the paper is published in. This is the date that should be used for referencing a paper.

Yes... but/and this formality is not a great reason to not give more forthright information about actual sequences/dates of events. I think it is a somewhat archaic stylistic affectation, etc. Truthfulness is usually a good thing.

@paulgarrett I think the suggestion that not including a date isn't "forthright" or "truthful" is a bit silly. It's an entirely practical problem - the author doesn't know the date the article will be published, especially published in print, until it is.

@EpiGrad Sorry, I meant the creation-date or submission-date, which are known to the author. These are of different interest than/from the publication date, which may be secondary in many ways.

The creation date is what is most relevant when we read a paper and want to know how current the research presented in it is. Right now I cannot think of a reason to leave the creation date out, except tradition (which should not be a good enough reason for us).

@clstaudt: What is the creation date of a paper? Often they take months to write. Is it the date of the idea? Or the date when the final version is submitted? Or after review?

@DaveClarke I would say that the date of the most recent modification to the paper does the job. Often, it does not even need to be more fine-grained than the year and the month to judge how current the research is. The date of the idea might also be interesting, but this is something that can be mentioned in the text.

My point is: When I get a paper it is very often in .pdf form and detached from the publication context (when and where it appeared first is not obvious). When I read sentences like "To our knowledge, we are the first to..." and "We review previous work..." I want to know how old the information is and how likely it is to be outdated. Why not make that easier?

Re completion date: because updating it manually every time you modify a draft is time-consuming and error-prone, and TeX does not really offer an easy out-of-the-box automated solution (mainly because of its inherent limitations as a programming language).
If you use a preprint repository such as arXiv, you have a submission date there, and that is good enough for most purposes.
Some journals list submission, acceptance and publication date, but that is a decision of the publisher, not of the author.

@CharlesMorisset: Correct me if I'm wrong, but there is not macro that will give the date the paper will be published, though.

\today gives the compilation date. If I take a document that I wrote 10 years ago and recompile it, \today expands to 2012. It would not be hard to check the file modification date instead, or get the date from some underlying revision control system, if only TeX were a sane programming language.

TeX is not a programming language. It's a typesetting language--and a versatile one at that, but at heart, it's still for typesetting, not programming (even though it was designed by a programmer!).

@CharlesMorisset iTeX will solve all that. Here is the Knuth presentation

Typically the date information is added by the journal.
In my experience most of the published work that is out there without dates comes from conference proceedings, where this information is given on the front cover but not on individual papers. I agree that it is a problem.


text:
How can I get the rights to my final year project?
I live in the UK, study Computing and I'm about to start my final year. I have been told by friends that the University holds the right to my final year project. Is there a way of getting the rights and intellectual property of my final year project?

Did you actually check with the University? What your friends tell you and what the University owns is often delineated by the fine print. At many Universities for example, the University retains a license to use your intellectual property, but you are still free to develop it.

The first question is why you want the rights.  For example, if you are working on something with serious commercial applications and hope to start a company or sell the technology, then this is a very serious issue.  The first step is hiring a lawyer, who can advise you on precisely which rights you and the university currently hold, and who can help you negotiate with the university regarding commercialization.
On the other hand, most student projects are of no commercial value.  If you just want to display your work online (to help build a portfolio for job applications and in case this work is useful for someone else), then it's probably easier.  It may depend on the university, but presumably they don't want to limit the dissemination of student projects, so if you ask them I bet they'll grant permission.  You should think about exactly what you want to provide and under what sort of license (for example, if you put code on the web, nobody's allowed to use it unless you license that).  I imagine the university would be happy with some sort of Creative Commons license.
I'd recommend being very clear and straightforward when asking, to avoid raising suspicions that you are trying to trick them into giving up the rights to valuable technology.

Before hiring a lawyer, I'd recommend talking to the University's intellectual property office (or similar) to identify exactly what their rights are. They might be draconian (retain all rights, including ownership) but Universities are usually more interested in helping their alumni get rich through their projects than they are in trying to develop projects for themselves!

I expect that it differs from university to university, but in general you won't be able to do this unless you buy the rights from them. Somebody in your students' union/student support services might be able to give you a better answer.

I would double-check on that statement of your friends. If you are not employed by someone to produce some intellectual property, then you will own the copyright to all texts and other material that you create. You are then free to transfer that right to someone else (at least in the UK), or give out licenses.
So unless either

you have a work contract with your university for this project, or
you signed an agreement that the university will own the rights to your project,

I would expect that you retain all rights in the project.
There is one caveat: Any material that is provided to you by the advisor of your project is of course not your intellectual property, and you would have to deal with it as with any external source. This may include even the initial project description, if it is of substantial intellectual value!


text:
Maximizing opportunities to be admitted in top schools
I did a modest undergraduate in Information Systems (3/4) and good master's in CS (3.4/4). I've PhD acceptance from a good school in Canada. However, I still need to go to top school , or at least a well-known school, in US.
I am planning to apply to top schools in CS next year (since deadlines already passed). I have done some research and got some papers accepted at good conferences. Beside getting good scores in GRE, what should I do to be well-prepared for the next year?
I am fully sponsored student by my government, how will this affect the admit decision?

"I still need to go to top school , or at least well-known school, in US" — You do?  Why?  Something wrong with Canada?

@JeffE OP is just worried our igloos won't be spacious enough for him, eh?

This has nothing to do with the beautiful Canada. It's because many of the recruiting committees members in my home country prefer US just because they have been there!.. Yes it's not an academic behavior but this is the case i'm facing.

Your approach is wrong and will be a hindrance in maximizing your chances for acceptance. No school wants to accept someone who only wants to go to their school because of its ranking. You need to tailor your application to demonstrate why you want to go to the particular school. Once you have identified some schools/supervisors, ideally one of your recommendation writers can introduce you. You then need to build on that relationship. Talk to them about how your work fits in with their past and current work. As your relationship with the potential supervisors builds, figure out how they fit into the department. They will likely have the inside knowledge needed for writing a really good application.

Let's take inventory. To respond to your order of presentation, your grades are so-so, not bad enough to keep you "out," but by themselves, not good enough to be a strong recommendation.
The next thing is: "I've done some research and got some papers accepted at good conferences." That puts you "ahead of the class" and probably got you into the good Canadian university. That will probably get you into many a good American university. As an American, I'd like to see you come stateside.
Perhaps the most interesting thing you said was that you are a fully sponsored (paid) student by your government. That suggests "scholarship student" to me, perhaps the equivalent of America's "National Merit Scholar."
In your applications, to universities, talk about how their programs meet the needs of your government, and why you'd be an ideal research bridge between the two. Many American universities are looking to add geographical and cultural diversity to their mix of students.  The fact that your government chose you as an "ambassador" is a factor in your favor.

It should be pointed out, however, that the core of the statement still needs to be about research, not about the funding.

@aeismail: Strengthened my comment to "ideal research bridge."

Grades are never "good enough to get you in", at least for the top schools OP is aiming for.

Many American universities are looking to broaden their contacts with key foreign governments. — Totally irrelevant. The university admins who are "looking to broaden their contacts" are not going to be on the graduate admissions committee.

@JeffE: I'd be very surprised if "diversity" weren't a factor in admissions. As in, "Let's take the borderline student from Idaho because of what s/he adds geographically, whom we wouldn't give a second thought to if the applicant was from New York City."

@TomAu Yes, diversity is an issue, but more for gender, race, previous educational opportunities (e.g., SLACs vs R1s). Geography, not so much. Why should we care if a student is from Idaho vs. NYC?

@JeffE: OK, I think I see where my "blind spot" was. Based on the name and reference to government sponsorship, I assumed that the OP was from Latin America, Africa, or Asia, (east, south or west). Probably not from the United States or Canada, but possibly from Europe (maybe even Eastern Europe). So I couched part of my answer to the point that "diversity" could help him.


text:
Should I sleep less to achieve my thesis targets?
I am doing my Masters (thesis-based) in Computer Engineering in Canada. I started my research in September 2015 and it is now the end of April in 2017 but I haven't done ANY significant research. It is very distressing and I definitely will need extra time to finish my research and graduate.
I meet with my professor and we both decide on what I need to do and a deadline is set for specific tasks. The initial stages of these tasks mainly involve installing software on my lab system which has the hardware I need for my research. I always run into problems during these installation processes and I end up spending more time than necessary JUST to have the necessary tools needed to do my project. By the time I get started with my work and do anything meaningful, the deadline arrives and the tasks remain incomplete.
My professor is frustrated by my lack of concrete results but despite that, he is encouraging and believes in my abilities. I also think I can publish at least one conference paper before I graduate. However, I am wasting my potential and my expertise by not meeting set deadlines. I know I can get things done but apparently, I am too slow in getting to where I want to be.
I feel that setting aside a set amount of time each day (6 hours or so) is not always effective in meeting goals. Should I just give up sleep (and definitely my leisure time) to meet my goals? I am afraid that it will impact my health and my concentration and negatively impact the quality of my work.
Should I simply come to terms with the fact that given my capabilities, I will need to sleep less to meet my goals?
EDIT:
I also work as a TA and a good amount of time also goes towards preparing for labs and marking students' papers.

Why can't you keep working on the project after the deadline? It seems ludicrous to keep missing unrealistic deadlines and then having to reset your work, if the deadline is set to just provide some structure for your research.

What next? Giving up eating?

I have done this before I used to go on less sleep and I would not recommend it. Granted you can get work done this way but you are young and this is the time that your brain is growing and if you mess up your sleep you're doing yourself a huge disservice. Try getting more time elsewhere. Also exercise and eat well for optimum performance. Good lick.

If the main thing that is slowing you down is difficulty installing needed software, then get some help with that, man!  There's stackexchange, there are computer gurus, there are fellow students....

Are you serious?!

Reducing sleep may work for a day or two. However, after that, sleep debt accumulates, and sleep deprivation will lead to a reduction in productivity.
Sleep is essential for your physical health, and in particular, it is essential for mental functioning. You may find it better to view sleep as a form of "work time". The cognitive structures you have about your thesis will be refined and pruned while you sleep. You'll make novel connections while you sleep. Sleep will also enable you to have the mental energy to engage in focused activity on the thesis.
In particular, the kind of deep creative thinking required to analyse data and write a thesis is helped greatly by being well-rested. Sleep also helps ensure that the work you do is directed towards your goals.
Thus, allocating enough time to sleep so that you are well-rested is essential to overall academic productivity.
So in general, if you are looking to maximise productivity in the medium-term (i.e., from a week or two to perhaps a month or two), then look at things other than sleep and thesis-time that can be trimmed. If possible, remove all other work commitments (i.e., no tutoring, RA work, consulting, etc.). Other work consumes largely the same set of limited mental and time resources that you have available each week. If possible, reduce non-work commitments.
Also, in the medium term, many people do pull back from social and leisure activities a little bit. But in the longer term, you want to think about a balance to your life that truly works for you. I also think that incorporating at least a moderate amount of physical exercise is also important.

I guess sleep, diet and exercise should be a part of one's lifestyle at all costs. But meeting deadlines is quite important. If time is used in doing work that is important but not directly useful, wouldn't that lost time have to be created elsewhere? How should I account for the time I lose in doing installations and setting things up?


text:
Will pursuing master degree increase the chances of Ph.D. admissions if the Ph.D. is in different field than Undergraduate is the goal?
I am a Pure Physics and Pure Math graduate. I wanted to do Ph.D. in Computer Science on AI. I am currently a research assistant on AI. if my undergraduate is not related to my area interest for Ph.D., will pursuing a master degree in CS increase the chances of Ph.D. CS admission? Or should I focus on research and getting publications and go directly to Ph.D.?
Are there any other disadvantages to go to master in different fields? Is it better to stay at undergraduate focusing more in research experience?
Related:
The first answer said that there are disadvantages getting M.Sc when applying to Ph.D. rather than staying in Bsc, but I guess it doesn't cover
the case when the Undergraduate and Ph.D. area are different.
Would getting a faster MSc instead of just BSc affect admission chances for PhD?

Did you apply and not get in?  Why not just see if the CS Ph.D. programs will take you as is?

Hi, I haven't applied but I want to have a plan since I need to save if I want to go for a master. But, thanks for the advice!

Your      CCcountry?

hi, I might want to go to the country in Europe or America.

Yes, pursuing a master degree in CS will increase the chances of Ph.D. CS admission.
If you show good research work in MS, then same advisor can help you get Ph.D. admission or other professors in the same or other universities who are doing research on the same or similar topic may accept you.

I assume you mean a master's in CS.
This might depend somewhat on where you are, but in the US it would probably have little effect. The way to learn if your background is adequate for doctoral admissions is jut to apply to a program or two. There are aspects of your education that would be good to have when studying AI.
In the US, I think that if you could get in to an MS program you could also get into a doctoral program with the same background. It might be different in EU or elsewhere, of course, especially in places that have strict rules.
But everywhere, you need to make your best case that you are qualified to begin and are a good candidate for success and that you have shown success in the things you've already done. You will find a lot of competition, of course, but no single thing will be determinative. Make your case.

At Michigan, it is much easier to get into the master's program in CS than the PhD program.  YMMV at different schools.


text:
What should I do if I am not able to reproduce the coauthors’ results?
We are doing computational biology research using ML. My coauthor who is a Phd student initially proposed a new idea that he said worked better than the baseline. However, after trying to replicate the result, I could not reproduce it. I have asked him repeatedly, but he seemed trying to avoid telling me how to reproduce the result and asked me to do something else. It seems to me that he is also not able to reproduce his own result and his idea does not even beat the baseline. Even when knowing that he could not reproduce his own result and his result did not make sense, he spent another 5 months on a mini project exploring this direction and he also kept pushing to submit the papers. Furthermore, the datasets that were used to train the models were not consistent, there is a new version of the dataset that is “easier” (due to random seed, and slightly different codes), but he keeps saying that the two datasets are the same and used interchangeably in the paper. I investigated, and the data was not the same and he was lying even to my PI.
I have worked for 2 - 3 years on this paper as a second or third author, but I am worried about working with this coauthor because I don’t trust what he’s doing. If I told my PI, the PhD would not be happy and may retaliate with more dishonesty. Despite the dishonesty, the PhD is very hardworking, so the PI may not believe me as well. What should I do? Should I take my name off the paper? or it is just a small matter and not a big misconduct? I have been working on this for 3 years, so I have a lot of sunk cost. This is my first paper and I want to use it to apply for graduate school. I also have an opportunity to keep doing the project and get a cofirst which will help my career and graduate school applications. Should I continue working with him? Or should I start over on a new project? I honestly have trust issues with whatever he’s doing, I don't know what’s true and not true anymore. I don’t like the fact that these kinds of people are more successful and have more papers than the average PhD..

To be clear: You're currently an undergraduate student? A year or so from graduating? What part of the world?

I’m a post bachelor RA with 5 years of experience in south east Asia. I worked on this project one year before the PhD came in.

"post bachelor RA" isn't understood everywhere. Are you enrolled in a degree program? If so, is it a masters or is it a doctorate?

@Buffy No, I am a full time RA after I get my bachelors degree. What do you think of this problem Buffy? Should I try to work with him or should I move on to the other project?

Before tossing accusations, talk to the PI or your major professor about your concerns.

@Part-timeEngineer have talked to my PI and eventually, my PI knows that the PhD's result is not reproducible. The PhD couldn't reproduce his own result.

@ivicts OMG, so it seems like a research misconduct is going on, if your PI really knows this. One thing I can assure you is that right now because of the development of AI, research misconduct WILL be detected, just a matter of time! I'd stay away from this research group and stop working with them. If I were you, I wouldn't even want my name on this paper. You are just an undergrad, you still have a long way to go. This is just my thought.

I think you're getting fine advice, so I won't answer further -- but I would like to know if your school is one of those that uses a real honor code.  In a place like that, your silence about a suspicion of dishonesty might be considered an honor code violation, which may certainly impact decisions you might make.

@Part-timeEngineer from what the OP has said, they are not an undergrad — they have a Bachelor’s degree and are now employed full-time with this research group as a research assistant. So this is more complex — the only way to stay away from the research group is to resign. Certainly, though, don’t put your name on this paper.

@Part-timeEngineer My coauthor who is a Phd student initially proposed a new idea that he said worked better than the baseline. This more complicated idea actually doesn't work better than the baseline. The PhD cannot reproduce the result that his idea actually beat the baseline, so he just adds a lot of things to the model that are just simply noise. This idea doesn't even make sense biologically, and my colleagues have pointed that out, but he's so stubborn and keep pushing for submission even when he himself couldn't replicate his idea. The PI was initially reluctant to submit the paper.

@Significance In the end, the reviewers are also suspicious about this idea, the paper gets rejected, and the idea that was not reproducible was removed, so the model goes back to my original model, but I went down from the second author to third author just because the PhD adds a lot of noise to the model that got us rejected. This paper is 3 years of work, if I take my name off, I have nothing after 3 years of work.. that's my concern. It's not like I have so many papers that I have the privilege to take my name off.

@ivicts Sir, I don't know which university you are working at and and which country you are living in. But if you have reported your suspicions about research misconduct to your PI and your PI just let it go without any action, then this is not right at all. Check website like PubPeer; research misconduct is exposed every day and every moment. So, for your own reputation, stay away from toxic research groups. Publishing a paper but based on the manipulated results, it is absolutely not worth.

@ScottSeidman I feel that I am too outspoken, critical & belligerent on this (among other things) and I got excluded, the PhD was reluctant sharing things to me now and I went from second author to third author. If I just went along and wait until the paper got rejected by the reviewers and telling them to go back to the right track, I might have a cofirst author by now.

@Part-timeEngineer that is what I disagree about with my PI. My PI was actually mad at this and mention to the PhD before his presentation to the group that he can't reproduce his own result and his idea doesn't beat the simple baseline. However, he still lets the PhD submits it. I feel that the PhD pushed my PI too hard on this because my PI is usually perfectionist, but as a PI he has power to do the right thing. Do you think adding a lot of stuff that doesn't work and not reproducible considered manipulated result? The new version of the paper doesn't have this idea though after rejection.

I am still confused whether I should try to work with the PhD. People say we should try to work with someone we don't like & we disagree with, how about someone we don't trust? Should I try to professionally work with him? or should I just stay away from him?

@ivicts Sir, I am not familiar with your field, and it is hard for me to say now.

Given what you say, the minimum is to take your concerns, along with the evidence, to the PI. If you are an undergraduate you will need to defer to their judgement.
As for leaving (or staying with) the project, that is a much riskier situation. As the "junior" partner and an undergrad, few would blame you, no matter what you do, but arranging a new project with a new PI takes time.
But if the doctoral student is lying about the research, it is a big deal. Make sure of your facts before you do anything.

Comments have been moved to chat; please do not continue the discussion here. Before posting a comment below this one, please review the purposes of comments. Comments that do not request clarification or suggest improvements usually belong as an answer, on [meta], or in [chat]. Comments continuing discussion may be removed.

I worry we've been understating things if you're concerned that not working with this charlatan is "too purist", as you said in the comments. If they're fabricating results, they're a terrible person and a disgrace to scientists everywhere. If you were to go along with it, you'd be a terrible person and a disgrace to scientists everywhere. I can't say whether you should definitely try to report them to the PI, the department head, and the editor of the journal (my inclination is to say go for the throat, but I understand if you don't have the clout to do that yet), but under absolutely no circumstances should you participate in this fraud.
The fact that you've already talked to the PI and the bad guy is apparently still trying to convince them to publish this suggests that the PI might be on your side here. Talk to them about it, and don't understate your concerns. Flat out say, "This paper claims that these experiments were done on the same dataset, and that's a lie."
Accusations of fraud are serious, and I could understand being reticent to make a public accusation without having all your evidence ready to go, but if you're just having a private conversation with your PI, don't worry about being diplomatic. Just speak openly and honestly about exactly what you've observed. They have the experience to know how bad this type of fraud is and what to do about it. You have the evidence that that's what's happening here. Provide every bit of information you have available so they can make the right call.
Two more things:

but if I’m able to find a way to work with him, I can get a cofirst author which will help me in my career, that’s the dilemma.

That's extremely dangerous thinking. Fraud usually helps someone's career; that's why people do it. Doing things that benefit you at the expense of others is almost the definition of evil. And this is at the expense of others. A fraudulent paper wastes the time of every honest scientist who tries to build on the work. In some fields (e.g., medicine, civil engineering), fraudulent research can kill people. There is never any excuse to fabricate data.

"I’m still wondering on how to go about this in a way that doesn’t alienate the Phd?"

When Houdini exposed the people running seances as frauds, he didn't make any friends among them. But why would he want to? They were scammers who took advantage of the naivete of others for their own selfish gains. Which of the two are better remembered by history? If you expose a fraud (and especially if you lose a paper because of it, although more likely, you'd just correct the paper so it honestly reports the real results), you will be viewed as a scientist who acts with honor and integrity by anyone whose opinion matters.

Would just being a third author mean "participating in this fraud"? I have talked to the PI after the paper submissions that some of the results are not reproducible. The PI did not say anything and called the PhD into the office to test the model and see which one really worked and not, but the paper got submitted anyway. After the revision, the PI said that everything is reproducible now. However, I could not check myself because I was excluded from the project since the PhD was not happy with me double-checking his work and knowing more than I should.

@ivicts If you're a coauthor, you're responsible for anything in the paper. If you know it's bogus and still attach your name to it, you're part of it.  If the PI said everything's reproducible now, maybe things got fixed? I don't know. You need to talk to the PI about your concerns and see if they've been addressed or not, I think.

since I am excluded, I am unable to take over. Well, the funny thing was the PhD went on on a mini project building on his result that he could not even reproduce himself, and then it was just a failure after 5 months. The problem is I alienated the PhD, was excluded from the project, and could not take over. If I just went along and waited until the reviewers rejected the papers, I could take over and ensure the whole thing is consistent and reproducible. So, I feel that sometimes if I just stay away from the paper, it does not help the cause..

I don't know.. but I need something in my CV after three years of work.. if I have no papers, it can end my career as well. Things got fixed after the rejections, but I am not in the project anymore to double check things. @Ray

Yeah, I don't know. I'm afraid I've given all the advice I can without actually seeing the data and the paper and talking the PI and...etc. If you're on good terms with the PI, they're the one you really need to have a conversation with until you're both satisfied that the paper is legit. (And if it's submitted but not accepted yet, there'll still be time for edits). For the conversation, maybe phrase it as you wanting to understand why the paper is legitimate instead of starting off by making accusations? That might help it go smoother (interpersonal stuff isn't exactly my forte, though).

I'm excluded from the project and not doing it anymore now.. I was given a project where I could be a co-first author partly because probably the PI felt bad that I was right all along but he excluded me, so I am focusing on that instead of a third author work. The sad thing is people who engage in this kind of fraud are more successful and get a co-first instead... where I'm a third author after exclusion

I know interpersonal stuff is not your forte lol because you sound exactly like me. Straight to the point, "purist" morally, and not diplomatic. Sometimes these things cannot be solved straight to the point the way we want it to be. Because alienating someone even if you are right will not help to advance the cause, there is a tradeoff somewhere..

Yeah. Well, if nothing else, at least remember this when you're at a point in your career where you do have the power to fight the good fight effectively.

Also, I read a lot of authorship dispute questions and I feel that the consensus is that maintaining professional relationships sometimes is more important than authorship. How about integrity vs relationship? If I spoke out about integrity, I would alienate someone one way or the other. Which one is more important integrity or professional relationships?

@ivicts I would say integrity. If it's an authorship dispute like "I should probably be first author but I'm willing to take second author if it'll keep the professional relationships running smooth", that's fine.  If it's an issue of honesty, though: integrity. If the results we report aren't true, then why are we even scientists?

so should I find a way to work with him despite the disagreement or should I just stay away from him completely and do another project with other people? he's very hardworking and motivated though..

Motivated to do good science or motivated to advance his career? Do you want to face a similar situation again? If there are honest people to work with, work with them.

For me, personally, I would stay away from them. But, people say that we should work with people with whom we disagree... so you mean this is not a question of disagreement but about ethics. For disagreement, we can still work it out, but for ethics, it's better to stay away from them?

and I don't even need to maintain a good relationship with them?

If the datasets are meaningfully different, they know this fact, and they reported otherwise, they are unethical and should be avoided (and reported, in a perfect world, but I'll leave that decision to you). If the datasets are different but they don't believe this to be the case, their competence is questionable, but we all make honest mistakes from time to time, so it's not as bad. If you point the honest mistake out and they hold fast to their view, then the question is whether you've adequately proven that the datasets are different. If so, the honest mistake becomes dishonest.

long story short, the PhD knew that the datasets were different but never told us (including the PI), I have confronted him about this. The PI actually thought I was the one who made things up because of this. When I said the datasets were different, I needed to make 20 PPT slides to show that the same models applied on different datasets yield different results because he denied it. After presenting, he's still pushing to submit the paper without retraining the model. So, it clears that he doesn't do thing in a good faith.

How can I cope that someone who has committed fraud can easily get papers out? They will be more successful and have more papers in high-impact journals as a cofirst than mine. I am here doing good science and can only get a third author...

@ivicts If crime didn't pay, people wouldn't do it. As for how to cope with it, I see two main options: you can recognize that doing good research is more important than getting first author and be satisfied with that. Low risk, low reward. Or you can try to bring down the frauds. I'm not sure what sort of whistleblowing procedures (and whistleblower protection) exist where you are, or what the risks are, but you might see if your institution has an office that handles that. If so, they can probably give way better advice than I can on what to do next.

@ivicts  If not, maybe inform the editor of the journal? Some countries and fields also have organizations like the Office of Research Integrity that can help.