Firsts: Submitting and revising a journal paper

This post contains the history of my first journal paper, “Multiple Instance Learning with Bag Dissimilarities” (also available via my Research page).  Recently I shared some examples of cover letters and responses to reviewers with people on Twitter, so I thought it would be informative to put it all together in one place, including a timeline of the process and take-home messages. Note that this is not a guide how to write a paper or how to respond to reviewers – but if you are looking for that Dr. Raul Pachego-Vega has lots of resources for this.

On with the story of the paper. The files (draft, original and revised submissions, cover letter, reviewer response) are all  here (.zip), but the post should be readable without them.

Draft to first submission

In my PhD years 1 and 2, I had a few workshop publications which were exploring different aspects of one idea, and it was time to put these results together into a journal paper. I made a first attempt to organize all my ideas in November 2012. This first draft then went through several iterations of discussions and comments with my supervisors. Finally, on the 25th of March 2013 I submitted to TPAMI. I think the plan might have actually been to submit to Pattern Recognition. But as I understood at the time, TPAMI was more impressive to have, and had a faster review process, so it was worth a shot.

When submitting, I did not consider anything else I would need other than the paper, like a cover letter! Therefore my cover letter was very short and uninformative. I only mentioned that the journal paper was based on earlier conference submissions, but not what the differences were. It seemed obvious to me that the journal paper was so different, that I didn’t need to explain this. Of course, after a few days I received an email (I remember having this stomach sinking feeling) that I needed to provide a summary of changes, which I did. It seemed my paper was still under submission – crisis averted!

Take-away: if the paper is based on any conference publications, explain the differences in the cover letter, even if you also do this in the paper

Rejection and another submission

The part about the fast review process was true. On the 5th of June 2013 I received the decision that the contribution was not significant enough for TPAMI. Since my paper wasn’t immediately rejected after submission and actually went to reviewers, I was quite satisfied with this result.

After updating the paper according to the useful comments I could extract from the reviews, on the 26th of June 2013 I submitted the paper to Pattern Recognition. Once again, the submission system caught me by surprise! While I now had a better cover letter, I now also needed to provide a “graphical abstract” and “highlights”.

Take-away: go through the submission system of the intended journal before you actually want to submit there. Another surprise I’ve encountered in other journals is that I could suggest names of reviewers – it is good to think about this beforehand, while you are writing the paper.

Major revision and responding to reviewers

As expected, the review process at Pattern Recognition was a bit slower. On the 23rd December 2013 I received a “reject and resubmit” or “major revision” decision. This was a more hopeful situation than with TPAMI, so I started revising the paper and writing my response.

A useful structure for the response is:

  • reviewer comment (in bold)
  • your response
  • quote from the updated paper which shows your changes (in a different text color)

Take-away: simplify the life of the reviewer, they likely do not exactly remember your paper and do not want to go through the whole thing, switching between the document and the updated paper, to see if their proposed changes have been made.

What I did wrong the first time around, is that I would do the suggested change in the paper and in the response, then would discuss both the paper and response with my supervisors. This was not productive – since they proposed changes to my change, I would have to modify two files!

Take-away: write the response first, include proposed changes in the response, then discuss with supervisors, then add changes to the paper!

Another annoying thing was that in my response I was referring to section numbers and references in the original paper. But since these would get updated (due to new sections or references), I would have to keep changing these by hand in the response. But, it turns out there are LateX packages for this too! See this answer on Stackexchange.

Besides the responses, we added a “cover letter” to the beginning of the response, explaining that we prepared a revision and summarizing the changes made. After a month or so, I submitted the revised paper! I was confused about filling in a “cover letter” text field in the submission system – after all, I now had a whole response to reviewers, that was a cover letter in itself. But I think I just copy pasted “cover letter” from the response, with a comment that detailed responses can be found in response.pdf.

Minor revision and accept!

Then finally, a long-awaited email came on the 20th of June 2014 – “We would be happy to publish your manuscript […] in the journal provided that it is revised in accordance with the enclosed referee comments.”

A minor revision! I remember exactly where I was at the moment – on a camping in Sweden, getting ready to celebrate midsummer. I was walking back from the bathroom to our tent and decided to check my email on my phone, and there it was. I’m pretty sure I jumped and yelled “yes”, or something of the sort. But it was great that I was already at a party, so I could celebrate this event immediately 🙂

Take-away: don’t forget to celebrate!

I sent in the revised version a few days later, and on 21st of July 2014, the paper was accepted, and in early 2015, published. A nice detail is that at the moment the paper was published, it already had a couple of citations – because I uploaded a preprint to arXiV back in 2013. See my blog post about this and a great post by Niko Kriegeskorte if you are still unsure.

Take-away: upload your papers to arXiV

Share your experience

Have you had a very long, or perhaps a very short review process? Surprises you encountered during the submission process? Or do you have any other tips about submitting papers you could share? Please leave a comment below!

On getting a tenure track position

As I announced a few weeks ago, I am starting as an assistant professor in the Medical Image Analysis group at the Eindhoven University of Technology.

The tweet is a bit of a technical announcement, but it encodes much more than “I have a new job”. Since I’m not good with threads on Twitter, I decided to share a few more feelings about this over here.

1. Excitement

I get to do research and teach and learn from others for the next 5 years! How amazing is that? I have so many ideas, I can’t wait!

2. Relief

I get to have a job for 5 years and don’t have to apply for positions for like, a very long time! I started looking for my next position halfway through my postdoc, which was a job in itself, and did not reflect well on my postdoc project. A few things were not really going well for me in 2016, so the news about the position couldn’t have come at a better time.

3. Fear

I worry they will discover I’m an impostor and they should have hired somebody else. I try to reassure myself by thinking that if I’m an impostor and they are the the real deal, they should have figured out that I was one already. But I also worry about just being able to handle it all.

4. Guilt

As many other researchers are forced out of academia, I feel guilty for “surviving” while having a “good, but not excellent CV” (citing reviews on some of my rejected grant applications). I didn’t have to deal with hundreds of rejections – I applied to four jobs, interviewed for three, and was offered one. Sure, I worked hard, but I think luck and privilege played a big role.

5. Hope

I get to be one step closer to maybe one day being able to change things, just a little bit.

Join me?

Over the past few months I came across profiles of people who recently started, or are starting their new jobs as assistant professors in 2017. I wonder if they are feeling the same things. So I thought, maybe we can start this thing where we meet online once a month or so, and share our experiences as we go? Please get in touch (email me, reply on Twitter or send a direct message) if you want to join.

 

Update 19th December: 

All fields are welcome and you can also join if you like this idea but started before 2017. I imagine we will a structured meeting once a month via Google Hangouts or Skype, and a private group (Google+, Slack?) for discussion in between meetings. I will gather names/emails for 1-2 weeks until we are with 5-10 people, and then I will send out an email with more details.

CV of Failure: Things I didn’t dare to try

Image by https://unsplash.com/@tersh4u

What counts as failure?

A recent #withAPhD conversation on Twitter prompted me to write a bit more about my CV of failures.

So far, I have been tracking the “quantifiable” failures, such as paper or grant rejections in my CV of failures, or shadow CV. However, there are a lot of other things that contribute to my experience of failure (and learning to deal with it) which are more difficult to quantify – because I have not tried them at all.

Most of these things can be summarized with the words “impostor syndrome.” I was convinced I would fail, or perhaps even worse, I was convinced “they” would laugh at me for even trying. But time and time again, evidence showed that I probably did have a chance. And even if I had failed, “they” would have thought it was good that I tried. It probably would have been better than always regretting not trying in the first place. So, what do I regret that I didn’t try?

Things I didn’t try

Although originally I thought only about purely academic things, I realized this pattern of not trying goes back much further. A few examples:

  • Talent show in high school. I’ve played piano for 7 years, but don’t consider it “talent show” quality, so I don’t sign up. At the talent show, somebody else is playing piano, but with many hiccups along the way.
  • First year of computer science at university. The student organization has sign up lists for different committees. The committee to organize parties seems fun, but I’m afraid it will have too many people, and I won’t be chosen, so I don’t sign up. Later I become friends with several guys who did join the committee, and realize they would have loved to have me.
  • Internships during my BSc and MSc. Several people are going abroad for internships. I’m afraid to get delayed with getting my diplomas. The projects I do in the Netherlands are all great and I get my diplomas on time, but the gap between the international experience I have, and the international experience that I could have, starts widening.
  • I’m writing papers during my PhD. The most competitive conferences such as NIPS seem to be way out of my league. I submit to good, but less competitive conferences and workshops. My first three papers all get accepted and I have a great time at the conferences. Later, I get evaluated on the quality of my publications – the places I’ve published do not really “count”. I read more papers from NIPS, and realize that maybe, I could have published there, too.
  • I’m finishing my PhD, and read all the regulations for graduating. A part of the regulations describe the requirements for cum laude. This involves a recommendation from the PhD advisors and several external reviewers. I ponder about asking my advisors, but decide against it. After all, even a graduate from our department who wrote several highly cited papers, didn’t graduate cum laude. “They” would find it ridiculous that I even brought the subject up. My defense is a success and the committee members are very positive. Later I confess to one of my advisors about my doubts, and he reassures me it would have made sense to at least try.

I learn from these events by recognizing the patterns and doing things differently the next time around. I did go on to participate in many committees, and even lead the student organization. The internship abroad was possible during my PhD. Although I still haven’t tried submitting to NIPS, I am now getting rejected often (and occasionally accepted) at MICCAI. I approach senior academics and ask for recommendations for fellowships and jobs. I am still scared every time, but past experiences tell me that it’s really much better if I try, than if I don’t.

Or, to quote Susan Jeffers*,

You’re not a failure if you don’t make it. You’re a success because you tried.

* Author of Feel the Fear… and Do it Anyway. The title alone is great advice.

CV of Failure: introduction

Image by https://unsplash.com/@tersh4u

My CV of Failure

Here it is – my CV of failure, or “shadow CV”.

I first found out about the concept of a CV of failure from this article. After a professor from Princeton posted his CV of failures online, shadow CVs have been getting more attention on Twitter, under the hashtags #ShadowCV and #CVofFailures. And it’s getting very popular too – the same professor now added a “meta-failure” of his shadow CV getting more attention than his research.

I already wrote about various successes and disappointments during my PhD (during my 3rd and 4th years). To write those posts, I used an Excel sheet that I normally use for yearly evaluations. Here is a screenshot from my 3rd year as a PhD student:

excel_progress

The one thing you can probably guess is that green is something that was successful, and red is something that was not. Creating a shadow CV would be essentially compiling all the red parts, over the five years that I’ve been doing research. In the era of tracking everything from what you ate to what music you listened to, why not track failures as well?

The experience

Given that I already had all the data, compiling the CV was quite easy. It was exciting – I was curious whether my shadow CV would be longer than a professor’s. It was comforting – the list wasn’t too long after all, and the inevitability of the list expanding in the near future didn’t seem as daunting. I also realized that it was good to start failing early with travel scholarships, because I feel more prepared now for the larger failures that I encounter.

But most importantly, compiling the CV was motivating. I thought about whether anything would have been different for me if I had seen such CVs a couple of years ago. As many other PhD students, I was not very confident. There were many things I didn’t even dare to apply for. Sometimes senior researchers would tell me these thoughts are unfounded, that I should just apply, and that everybody gets rejected. Sometimes I listened, and sometimes got rejected, but sometimes got accepted, which ultimately gave me more confidence. I hope that seeing shadow CVs can help other students do the same: go for more opportunities, fail, and learn from it.

Year in review: final year as a PhD student

This post is a summary of 2014, the last year of my PhD. I am writing it a whole year later due to my difficult relationship with blogging. There are two reasons for this: a recent conversation about blogging on Twitter, with this result, and the fact that the summary of my third PhD year played an important role in me deciding to resurrect this blog.

As 2013 was a year of submitting papers, I expected that 2014 would be a year of paper resubmissions. That guess was quite accurate. But 2014 had more challenges in store for me. The year didn’t start out great for me for personal reasons. I am not sure I will ever discuss the details online, so let’s just leave it at “life changing event”. Up until that point, I was sure I would finish my PhD on time. But, with so many things changing so rapidly, I started having serious doubts about my progress.

Writing and staying motivated

Despite the personal chaos, I continued to work on the revisions of my rejected papers. In February, I resubmitted Paper 1. That was tough, so I didn’t want to touch the other rejected papers for a while. Besides, I had other activities lined up, such as a research visit to Copenhagen, where I wrote a conference paper about the work I had done the year before. The visit was a great experience, both professionally and personally! Unfortunately, I received a rejection, adding yet another thing to the revise-resubmit list. On top of that, I was rejected for the Anita Borg scholarship for the third and final time. But there was also a bright side: for example, around the same time I gave my first invited talks, which was a much-needed boost for my confidence.

In June, I finally received the coveted “We would be happy to publish your manuscript” email about Paper 1. This gave me the needed motivation to continue with the other revisions. In July, I resubmitted Paper 2, and in September, Paper 3, which by then had already been rejected at two different journals. Again, it was very helpful to be involved in other activities, such as organizing a workshop and teaching, to stay motivated.

With one accepted journal paper and two others under review, I again started hoping that I would submit my thesis by the end of the year. The thesis requires at least four chapters, each based on a “publishable” paper. My supervisors agreed, so I spent the last months working on Paper 4. Paper 4 described recent results, and was therefore very refreshing in the midst of all the revising. I finished it on time and submitted it to a conference in December. And then, with three papers “in limbo”, both 2014 and my PhD contract, ended.

Take-aways

My year of revisions had a few successes and several disappointments. However, the more important successes were the things that these experiences taught me. I…

  • …became a seasoned reviser-and-resubmitter
  • …learnt how to stay confident as a researcher despite a lot of disappointments
  • …realized even more deeply how important it is to have colleagues who believe in you, who support you, and who are up for a grabbing a beer (or a Spa rood), whether it is to celebrate or offer a shoulder to cry on.
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