Multiple Overleaf projects with a single .bib file

I recently discovered that one of my biggest dreams – being able to link all my online LateX projects to a single .bib file (but without using Mendeley) – is possible!

Previously I had “solved” this problem with ShareLateX projects, by writing a script that copies my main .bib file to several project folders every hour. However, this requires Dropbox sync for ShareLateX, which is a premium feature for new users. Not to mention, it’s not ideal to do it every hour, and to have to update the script when you want the .bib file to be copied with an additional project.

Now a much simpler solution is possible with Overleaf. It’s probably been there for a long time, but I only realized this now. When you add a new file to an Overleaf project, there is an option “Upload from URL”. I thought this option would do just that – get the file from the URL and upload it. But what it actually does, is remotely link to the file. That’s the solution right there! (Thanks to Overleaf’s Dr. LianTze Lim for pointing this out!)

Here are the steps to get this to work:

1. Put your .bib file in Dropbox, set the sharing settings so that it’s accessible by anyone with the link. Copy the link

2. In your Overleaf project, Go to “Files”, then “Upload from URL” and paste the link here. With Dropbox, this link will end in “dl=0”. Change this to “dl=1”

If this works correctly, you should now see your .bib file in your project, but with a “linked” icon next to it

3. Proceed as you usually would with a bibliography file

If you are collaborating with others, the best way is probably to have two .bib files – the linked one (not writeable from Overleaf) and another one that is local to the project, for any new references. This way at the end of the project, you could move all the new references to your main .bib file.

I also tried to do this in ShareLatex, but couldn’t find this type of option. Although ShareLateX has free Dropbox sync because I’m an early user, this feature of Overleaf could have convinced me to switch (even if losing the sync). But Overleaf and ShareLateX are merging, so I’m hoping I might get to enjoy the benefits of both.

How to find medical imaging companies (in the Netherlands)

A slightly different type of post today! Inspired by Dr. Raul Pacheco-Vega, who writes many of his amazing blog posts for his students, I decided to write about a question that has already come up a few times, and will probably come up again. The question is – where can I find companies who do (medical) image analysis (in the Netherlands)? This is important for students looking for internships, graduation projects, and jobs.

In this post I outline my search strategies to find such companies – especially small ones, which are difficult to find otherwise. These strategies might be useful to you even if you are searching for companies in other fields or countries.  The strategies are based on searching online, so they don’t assume you already have a network of people to rely on.

1. Who is advertising for jobs

The most straightforward way is to search for keywords on LinkedIn. If I search for “medical imaging” in the Netherlands, I get a lot of vacancies at Philips and a few at research institutions. There are also several vacancies which do not have a connection to medical imaging.

My intuition is that this type of search would overlook companies that do not have a specific vacancy, but would welcome open applications from people with the right qualifications. The same holds for internships – often these are not advertised on any website, but there might be opportunities if you contact a company directly.

2. Where are alumni working

The next place I’m going to look, is where alumni of biomedical engineering at Eindhoven University of Technology (TU/e) are working. Here is a LinkedIn page with alumni of TU/e.  I cannot filter by faculty here, but I can enter search terms related to the names of the programs offered, for example, “biomedical”. I can also filter for alumni living in the Netherlands, and filter by date to filter out any current students.

Now I just click on a lot of profiles, if the description suggests the person is working in a company, and screening the companies for doing (medical) imaging. This is quite a time-intensive process. There are many companies that hire biomedical engineering graduates, but that do not focus on imaging. But I did find many more examples than with the first strategy:

3. Who is sponsoring the conferences

Moving away from LinkedIn, a way that helped me discover several companies, is through sponsoring at academic conferences. The first step is to find out what the main conferences are, either from reading papers or searching online. For medical imaging I’m going to look at MICCAI, which has been running for 21 years, but also a a new conference MIDL, which is held this year in Amsterdam.

Now simply search for a “Sponsors” page and you are good to go! Some conferences (or rather, professional societies that organize the conference) also have a dedicated job page, for example the MICCAI job board. Here are the results from the sponsor pages (not limited to the Netherlands):

 

4. Who tweets about it

Of course this post would not be complete without Twitter! First I’m going to try searching for keywords, starting with “medical imaging”. If I then click on the tab “People”, I see accounts who have “medical imaging” in their bio. This list already includes several companies, for example:

Another strategy would be to look at the who follows medical imaging researchers and companies. The trick is to find an account with not too few, but also not too many followers. In this example I will look at who follows Quantib, a company based in the Netherlands. From the list of followers, I find the following:

These accounts should also give you some ideas of what other keywords or hashtags to search for.

I hope this was useful! Happy internship / job searching, and please comment below if you have other tips!

Balancing responsibilities in academia

In this post I discuss how I divide my time as an assistant professor and whether it is any different from being a postdoc or a PhD student. This is inspired by this tweet by @jayvanbavel (the plot is from this presentation), that got quite a lot of attention. Since I also had a few questions from readers about how I balance my responsibilities, I thought this would be a good topic to talk about. Spoiler: I do not identify with the message of this plot.

The categories in the plot are very fine-grained, but I will just talk about the larger categories: research (which for me includes manuscripts), service, grants, teaching and advising.

https://twitter.com/jayvanbavel/status/980071519505338369

As a PhD student

It’s true, as a PhD student I spent most of my time doing research. I would have whole days just for my exploring papers, drawing things on paper, trying out things in Matlab, meeting with my supervisors and writing down my findings. I suppose that going to talks also counts as “research” in this categorization. But more often than not, I did spend time on other categories than research and manuscripts.

First there is teaching. In my department, PhD students did not have to do a lot of teaching, but would be expected to help out with practical exercises in various courses. I did that, and volunteered for other teaching opportunities. I gave a few lectures about my research topic – the first took me approximately 30 hours of prepare. I’m quite shocked at this number now, and think I must have miscounted, but I did blog about right when it was happening, so I should probably trust my past self. I also had an opportunity to help redesign a module of a course, which was very insightful, but was also time-consuming.

Then there were activities in the “service” category. I had started reviewing papers, organizing workshops and giving outreach talks. I also organized the lab meetings for a while and kept various websites up to date. I enjoyed these activities and never consciously thought of them as “taking time away from my research”, which is probably why my grant reviewers are complaining now about my publication record.

The only category I didn’t spend a lot of time on was “grants”. But even so, I did manage to get a few rejections in that time.

As a postdoc

Most of the activities I was doing as a PhD student, continued into my postdoc, so it definitely wasn’t mostly “research”. While teaching decreased a little bit, service definitely increased – not because of the obligations of my contract, but my perceived obligation to the community, for which I was reviewing etc.

The big difference was “grants”. I had a two-year position, but given the low probability of getting funding, I started applying for things 6 months into the position. Since most things were rejected, this did take a lot of time away from research, and further worsened my position with grant reviewers.

Sometimes I hear the advice “only spend time on research during your postdoc and don’t worry about grants”. It’s nice to think how things would be now if I did have more publications from my postdoc. But at the same time, if I didn’t do what I did, I probably would not have the job I have now.

As tenure track faculty

In my current position, I am for the first time expected/paid to do all the things I was doing before  – research, teaching, advising, service and grants. I think if I had spent the previous years doing only research, this would have been a very difficult shift. But having a bit of experience in each area has helped the transition a lot, even though my research did suffer compared to my PhD.

I am not sure what % of my time I spend on each category because this varies per week. But I do – for the first time – consciously think about it.  I say no more often now (especially in the service category – while still doing my fair share). I try to group meetings, so that I have a few days without meetings, which I can then dedicate to research (although I do get distracted by other things I’m involved in).  My weekly review, where I write down what I did in different categories, also helps to see whether I’m spending too little time on research.

All in all, balancing responsibilities is difficult, but I feel that it’s possible to learn to do it better, which is one of the things (I realized) I’m exploring on this blog. I feel very fortunate to have the support – from colleagues, mentors and the community on Twitter – to do so.

I would love to hear from you – how do your spend your time, and has this changed throughout your career?

Writing a PhD thesis in the Netherlands

This post summarizes the process I went through to write and publish my thesis in 2015 at the Delft University of Technology. From what I understand, my experience is representative for computer science and other technical PhDs in the Netherlands. I am not sure how things generalize beyond that.

PhD by publication

In my department it was standard to do a “PhD by publication”. Although you do have a formal thesis in the end, the goal is to publish four first-author journal papers in the four years of your employment. These papers would go “as is” as four chapters into your thesis, and you would add two general introduction and discussion sections to complete it. You could of course also add other chapters if you have more papers or want to add unpublished material.

Different groups have different guidelines on what counts as “publishing a journal paper”. Peer-reviewed conference papers, or papers that you have submitted and are under review at a journal, could also count. My “thesis” was approved when I had 2 accepted journal papers (but, one of these was a second-author paper), 2 journal papers for which I had submitted major revisions, and 1 conference paper that was under review. I write “thesis”, because at the time of approval I didn’t have a single document called “thesis.pdf”, but an outline of which papers would become chapters, and their status of acceptance.

 

Writing

I think that when I started my PhD, I was aware of the PhD by publication, but I thought I would write a “real” manuscript to satisfy the perfectionist within me. But I changed my mind when I realized that’s the only result I would accomplish – my PhD would count just as little or just as much. Since I spent the last year of my PhD revising papers, I was quite happy to choose the easier (but just as effective) option.

There was not a lot of writing to do – only a general introduction and discussion chapters. I got started about 9 months before my contract ended, but I definitely didn’t work on my thesis full-time. I do think it was good to start early, because it gave me some time to digest what I’ve done in the years before and gain new insights. Perhaps that is a disadvantage of a PhD by publication, because it does not “as naturally” lead to taking a step back, as I would imagine you need to do if you have to write an entire manuscript.

I also appreciated having the 9 months to write my propositions, which I defended together with the thesis – see my earlier post about this.

Next to writing two chapters and propositions, I just put together the papers I had into a single LateX project/template. I spent a few hours battling with incompatible packages, but after it compiled, it was amazing to suddenly see all my papers form 100 or so pages of thesis.pdf.

 

Approval

After getting thesis.pdf approved by my supervisors and the plagiarism check of the university, it could be sent to my thesis committee and I could plan a defense date. I believe this happened around January 2015, and my defense was scheduled for June 2015. I’m a bit foggy on the details on this, but I think at this point it is assumed that you will in fact successfully defend your thesis.

In the time in between, you could get comments from your committee on possible revisions, and when enough committee members approve, you can go ahead and print your thesis. In my case, two committee members had suggestions for revisions. One committee member suggested a few points for the discussion, but also said that the thesis was approved regardless of whether I had time to implement them. The other commitee member essentially wanted a “major revision”. But, this committee member responded way after the deadline, so since all the other committee members had approved, I had already printed my thesis. Talk about a scare though…

 

Publishing

Before the defense, you have to publish/print your thesis. There are several companies that specialize in this, and you get a bit of budget from the unversity to do the printing. The main things you need is a thesis.pdf that is formatted correctly (not a problem since my latex template already took care of that) and a cover.

I spent quite a bit of time thinking about my cover – since I wasn’t working on a specific application, it was difficult to come up with something that would illustrate my topic. Once I had the concept in mind, my friend Hella Hekkelman made the illustration for me – I’m still very happy about it:

Here is it in action:

 

To see more examples of cover design, check out another friend Carolyn’s post how she designed her own cover.

With the thesis and cover, I ordered about 120 copies of my thesis from the publisher. This is a a relatively normal number, since you give copies to people from your department or in your field. I have even heard of people printing 300 or more! But, everybody advised me not print too many, so I got exactly the amount that the university budget would cover. In retrospect, I wish I would have invested a bit more into it, because a year after my defense, I had already ran out of copies.

***

Update April 2019: If you have cats on your PhD cover, definitely order more! Proefschriftmaken.nl was kind enough to give me a discount, and I just ordered 30 more books! 

 

Reader Q&A – Applying for a PhD position

In this post I’m answering a question from a blog reader – What qualities do you look for in a PhD candidate?

I have never hired any PhD candidates but I share a few thoughts of what I think I would pay attention to. This is also an interesting “time capsule” experiment for me – I hope that I will be able to reflect on the list below in the future.

This post is based on my experiences in the Netherlands, where PhD positions are jobs, and there is no single “grad school application” process that might exist in other countries. To apply for a position, you would be asked to send in your CV, list of subjects, motivation letter, reference letter and perhaps a summary of your MSc thesis project. At least, this is what I had to submit to apply to my PhD position back in 2010.

Evidence of problem solving

Probably the most important factor that I would look for is that you have experience with solving problems and completing projects. A MSc thesis, or a summary of your ongoing thesis, is a good example.

Other projects also count, but this needs to be clear from your CV. Simply having “machine learning” on your list of subjects, and “Python” on list of skills does not tell me if you can get started if I give you a dataset. A short description of a concrete project you did gives me more information. If you can link to a github repository – even better. Reference letters are probably also good places to look for evidence.

Interest in position

I want to know what interests you about the research topic, why you want to do research and/or why want to work with me. Mentioning that you find topic X interesting, is not enough. Ideally, your motivation should indicate that you have given the topic some thought, for example, by thinking of possible research questions.

A simple way to score points on this, is to follow the instructions of the application process and proofread the materials you send in. This shows that you invested a bit of time into the application and are not applying for any (not relevant) position that’s out there.

Other interests

Personally I think it’s a good thing to have more interests than what you study at university. This can include elective courses, organizing events, a blog about your favorite hobby… Again, short descriptions of what you achieved are better than listing a number of activities as hobbies.

Although not directly related to research, I think these things indicate something about independence, curiosity, and being open to new ideas.

“Team player”

Last but not least, it’s important that you are respectful of others, reliable when you promise others to do something, listen to feedback and help others out. This is probably the most difficult assess from an application, but I imagine that reference letters should say something about this, and if they don’t, it’s an option to contact the referee and ask.

Qualities I find overrated

Probably an unpopular opinion, but I find some qualities that are traditionally considered important, overrated.

The first one is having high grades. Sure, it doesn’t look good if all your grades are just above a pass. But there are many reasons why some grades can be lower – having a job to be able to afford to study, illness, poor course setup. So I wouldn’t dismiss an application just for that reason.

The second one is descriptors like “highly motivated” in the motivation letter. I realize that such statements are dependent on your background/culture, and on how much training you got in writing the letter. I think these are not good predictors of whether you can complete a research project.

***

I would love to hear your thoughts – am I missing essential qualities or putting too much emphasis on others?

And if there is a different question you have for me, please get in touch so I can answer it in another Q&A post!

7 things I’m glad I did during my PhD

7 things I'm glad I did during my PhD

After the 7 things I wish I would have done during my PhD, here is an opposite list of PhD advice – of things I’m happy I did, and I would recommend to others. It is also a bit of a “trip down memory lane” of this blog, as I realized I have written about most of these experiences before, but never connected them together. Enjoy!

7 things I'm glad I did during my PhD

 

1. Choose based on people, not on project

I applied to only one lab for my PhD (an earlier post about this). I applied there because I knew I was going to have a great time for four years, and that is largely because of the people in the lab.

Of course I was interested in machine learning, but within machine learning, most topics would have been interesting. The topic of the position I was applying for – “Dissimilarity-based multiple instance learning” – did not tell me much at the time. It was already during my PhD that I got really excited about it, and that is why I have a thesis with the same title now.

I also have to note here that in my experience, if you are in a good place, you will have freedom to pursue your own ideas as well.

 

2. Treat it as a job

Although this seems to be a controversial idea (e.g. professors tweeting that PhD students who don’t put in 80 hours a week “should not be there”), it is entirely possible to treat a PhD as a “normal job”. You know, with things like weekends, sick leave and holidays.

A factor that definitely played a role in my attitude is the system in the Netherlands (and several other countries) where PhD researchers are not students, but employees. It is of course easier to go on vacation or take sick leave, when you don’t have to worry about paying your bills or getting fired.

But perhaps more importantly, I was fortunate not to encounter anybody with the 80 hour mindset. I set myself the same hours as that I saw my supervisors in the lab (roughly 8:30 to 17), and went home after that. I realize now they probably worked at home too, but I never felt the pressure to do so.  See also the point above on choosing for the people, not the project.

More generally, I think it’s good for your mental health to have an identity that is separate from being a researcher, to help deal with failures that will inevitably occur.

 

3. Go to a conference early on

For the first month of my PhD I actually worked on the topic of my MSc thesis, to write a paper for a small conference. It’s not a “big deal” conference, but I cannot stress enough how important this experience was.

First, this meant that I started practicing writing papers (and getting feedback, from supervisors and from reviewers) very early on. Although the topic of my PhD was different and so I couldn’t use the publication for my thesis, the skills I learned still applied.

Second, just a few months into my PhD, I went to a conference where I recognized all the senior people from their badges. And, it being a small conference, several of them talked to me and complimented me on my presentation! This is huge deal if you are, like many PhD students, dealing with some form of imposter syndrome.

Last, I really enjoyed the atmosphere at the conference in general. This motivated me to do a lot of conference paper writing in the following years (such that I was a bit late with realizing I had to also write journal papers, which I do not recommend).

 

4. Do not only do research

Teach, organize a workshop or review papers – something else than your main project. Yes, these things technically “take away time” from your research time, but in my experience they:

  • Give you experience that will be valuable later on (possibly also outside of academia)
  • Give you a productive thing to do when your writing just isn’t progressing
  • Help you stay motivated

In the end, although I spent time on these types of activities, I think I gained time because I could return to my writing with more energy, rather than beating myself up and starting at the screen for hours.

With that being said, also do not do too much – maybe one extra project at a time. If you start doing these things and people realize you are able/happy to do them, you will get more requests, so prepare to say no (something to add to my “should have” list).

 

5. Have an online presence

Although I regret not using Twiter or blogging more, I did do my best to be findable online. I kept my university page and Google scholar profiles up to date, and uploaded my papers to the university website and ResearchGate.

When submitting papers to journals, I posted them on arXiV. For example, I submitted 3 journal papers in 2013. They were only published in 2015 and 2016 (!), when I was already a postdoc. However, these papers have been gathering citations since 2013 (not many, but I’m very proud/excited about it nonetheless). In 2015 and 2016, as recent papers with already a couple of citations, they might have been seen as “important to cite”, leading to further increases in citations and allowing me to benefit from the preprint citation bump.

If you are thinking “none of this is necessary if you just do great research”, evidence suggests otherwise. For example, you are less likely to be cited if you are a woman in international relations or astronomy.

 

6. Visit another lab

Visit another lab for a few months – most would recommend going to a different country too, but if your situation doesn’t allow that, I think going to a lab in a city close by would also be valuable. Apart from the obvious benefits of learning new things, collaborating on a project, and sharing your research, for me visiting another lab has been essential for finding mentors and becoming a more confident researcher. I wrote about this in the post “A few thoughts on mentors”.

7. Bring your own lunch

Yes, it costs time in the morning or the evening before. But it is healthier and cheaper, and much more rewarding!. Lunch in the Netherlands isn’t that great anyway – the standard is to eat bread with something on it (typically not avocado).

The better alternatives are probably at least EUR 5 – I would estimate 2-3 times more expensive than my (sometimes even containing avocado) lunches. If you do this for 4 years you probably still won’t save enough money for a deposit, but you will gain a habit that will in turn help you adopt other useful habits – writing, perhaps?

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Do you have any PhD advice you would like to share? Please let me know below or via Twitter!

Reverse engineering your CV

I recently discovered a great podcast called The Startup Scientist, of which I have now swallowed up all episodes – thanks to Daniel Lakens for the recommendation! The podcast is about treating your academic career as a start-up. I have made this comparison before when giving talks at career orientations but wasn’t able to distill this idea, so I was excited to discover that Dan Quintana did exactly that, so now I can add on to it in this post.

The episode I want to write about is Reverse Engineering your Career Goals. Although I do often say that my career so far is a series of coincidences, I do think this type of reverse engineering has played a part in it.

Towards the second half of my PhD I had a lot of doubts about continuing in academia – I really wanted to, but I was aware that it would be very difficult to get a position. I wanted to do a postdoc, but only if I had a reasonable chance of getting a position afterwards. I was not sure how to estimate this chance, so I used the approach below.

 

1. Find representative data

I first studied the CVs of Dutch professors I knew, and concluded that most of them received independent funding a few years after their PhD. But these professors were already professors for a few years, so I decided their situations did not apply to me.

Through the funder’s website, I found a list of people in related disciplines who received this type of funding that year. Since I was a year away from finishing my PhD, and these people got their PhDs maximum 3 years ago, the gap between me and them narrowed.

 

2. Generalize

After searching for CVs of my “prototypes”, as a good machine learner I tried to find patterns. Although the people were all quite different, and I only had a few examples (I wasn’t doing this automatically, although that would have been an awesome side project), it was easy to spot several things they had in common.

I did this during my pre-Evernote era so sadly I do not have notes on what exactly I discovered, but I do remember two things in particular:

  • All recipients had an impressive (at least for me) h-index. The minimum I found was 6, but the values between 9 and 12 or so were more common. This will vary per field, but for context, the professors I thought were not representative, would be in the 20+ category.
  • Many recipients had an extra “thing” that was different from most others, like their own company, an organization they volunteered for, etc.

3. Multiple time points

Next to looking at people’s websites, it’s also helpful to search for “Name CV filetype:pdf”. Using this method, I was also able to find CVs of the same people, but from a few years ago. This had several benefits.

While the current CVs looked quite intimidating to me, the “time travel” CVs were much more relatable. Instead of learning only about the “value” of a CV, I was now learning about the “gradient”, which would be easier to apply to my own situation.

Of course, it is possible to do this for any CV, by removing all the things from the recent years. But the nice thing about the real “time travel” CVs was that I also saw how people changed the way they presented the same thing, that both CVs already had. For example, a side project that might have been insignificant in the “time travel” CV, was described in more detail in the current CV.

4. Predict?

Now that you’ve estimated your function where the inputs are the CVs at different time points and the output is receiving funding, you could try to fill in what’s missing from your future CV, to get the same output.

Don’t forget that there are multiple solutions (so different inputs will lead to the same output) and noise (so the same input might lead to a different output). Since I’m on a roll with this analogy – there are also lots of other inputs that you might not even be considering yet (life and stuff).

I did not actually create any concrete plans of what I was going to do, based on this informal study. But I suppose that the information got deposited somewhere, and helped me make choices that would later point me in the direction of a solution.

A few thoughts on mentors

As promised, a post on finding mentors and being a mentor. This is something I’ve been thinking a lot about recently, so it’s difficult to distill everything into a structured post – but here a few thoughts / tips that might be helpful.

1. You need more mentors than only your supervisor

Even if you have the best supervisor in the world, they will not know all the things you might need advice on, like time management, planning your career or putting your health before your project. This is even more true if your background is different from the supervisor’s, and they have never been in the situation you might find yourself in.

Therefore it’s important to find other mentors who are more similar to you. Gender is an obvious characteristic that comes to mind – here are studies showing that women assigned to women mentors are less likely to drop out of science and engineering, or more likely to become professors themselves.

I think this is similar to my experience. As I have written before, I had a great advisors during my PhD. I would have probably laughed if I had to join a mentoring program and meet with another professor, just because we both happened to be female. But I do think that meeting some amazing women mentors along the way, is what convinced me to give a career in academia a try.

That being said, there are other characteristics that can define what similar means for you, but are more hidden, such as being a first generation student or having a health issue.

2. Mentors can be anyone

A mentor doesn’t necessarily have to be a more senior person in the same field. If you see the word mentor as “a person you can learn something from”, it becomes easier to think about this. Here are some (perhaps less traditional) examples of who I consider mentors:

  • Assistant professors in different fields related to computer science. We have a Slack group where we share advice, our failures (#rants) and successes (#humblebrag).
  • Students who I do not supervise, but who inspire me because of how they approach their work and/or life, and/or who teach me how to be a better researcher and supervisor by sharing the experiences they have.
  • Academic community on Twitter, where lots of amazing advice is shared.

Note that most of these people probably do not consider themselves as mentors in these situations! These conversations do not start with “will you be my mentor?”, but with genuine questions about a particular topic, that the others might have more expertise in.

 

3. Be a mentor too

Since anybody can be a mentor, you can be a mentor too!

If you want to benefit from others’ mentorship, you have to be able to offer something in return. This might be difficult to imagine if your mentor is more senior, but they can probably still learn something from you too. If this still does not apply to you can pay it forward by mentoring other students.

In all cases, be a good mentee – here’s a recent thread on the subject:

Finally, I’d like to share this post on service as leadership – mentoring isn’t a chore you have to do, but an amazing opportunity you get to do.

 

7 things I wish I had done during my PhD

Every so often there are threads on Twitter about what people wish they would have would have known before starting their PhD, or would have done differently in retrospect. Here is a thread with lots of great advice by David Schoppik and another one by Jennifer Polk. I haven’t responded to either question, because there is so much to say that I can’t fit into 140 characters. However, I have already been keeping a “wishlist” of sorts, so I thought this was a good opportunity to finally turn them into a blog post. Here they are, the things I wish I had done during my PhD.

1. Having a lab journal

I somehow managed to miss out on this concept completely. Maybe I had heard about it, but dismissed the idea because I didn’t work in a lab. I only really found out about it when I was about to start my tenure track position, and was reading “At the Helm” in preparation.

Sure, I had a notebook. I would use it to make notes in meetings, draw toy datasets, write down tasks as they came up… anything, really! But none of these things were intended for anybody else, including the future me, to read.

In retrospect, it would have been helpful to have a central place to record ideas, different (failed) experiments, and where I ended up storing my data and code.

2. Having a todo list

This might be a surprise to many, but I didn’t have really have a todo list during my PhD. I would write down tasks as they would come up – for example “prepare presentation for lab meeting” – in my notebook. If I didn’t get a task done 2-3 pages later, I would copy it over to the current page I was on.

I don’t remember forgetting to do anything important and I didn’t miss any deadlines, which probably gave others (and myself) an impression that I was an organized person. But the 2017 me is overwhelmed by the idea of this “organization system”.

3. Spending more time with other PhD students

I don’t mean with this point that I didn’t spend any time with friends or colleagues. I did my PhD in in the same city as where I got my other degrees, so there were lots of friends around. And I was in a great lab, where we would often do social activities together, and would see each other as friends. I realize that I’m very lucky to be in this situation.

But most of friends were not doing PhDs, and with my colleagues, often it was more relaxing to talk about topics outside of work. So it was great to meet other PhD students, for example during courses, and share experiences about writing, teaching… anything that might have been challenging. I should have done that a lot more! Maybe I would have learned about “lab notebooks” and “todo lists” 🙂

4. Seeking out more mentors

As I wrote above, I was in a great (though perhaps small) lab. My supervisors were both inspiring scientists, and very kind people. But even despite these favorable circumstances, I didn’t always dare to tell them what was on my mind. How was I doing with my research? Was my CV maybe good enough to apply for this scholarsip? Did I have good chances of getting an academic position? Questions I was too scared to ask, because I thought I would be laughed at, even though I logically knew that wouldn’t happen!

But things changed a bit when I did an internship, and met two very different mentors. They were closer to me in age and career step – both postdocs at the time – and were women. They saw right through my self-esteem issues, and made me a bit more confident that I wasn’t entirely delusional about my aspirations.

 

5. Applying for all the things

In the Netherlands, as a PhD researcher you are an employee, not a student. I had a salary and my travel expenses were reimbursed. Therefore I never felt the need to apply for any financial support.

As for awards, most of the time it either didn’t cross my mind I should apply, and if it did, my imposter syndrome didn’t let me. It didn’t help of course, that the one scholarship I really thought was a good fit (Anita Borg Memorial scholarship) was rejected three times in a row.

In retrospect, I think applying for more things would have made the applications I really wanted, like the Anita Borg one, a lot better. Not to mention the benefits for applying for larger grants later on.

 

6. Joining Twitter

Although I had an account for years, I didn’t start using it until half-way through my postdoc. Maybe a funny story is that this all happened because of a grant I applied for. The best submissions would be advertised via Twitter, so I thought I should at least see what people are saying about my submission (not much). But since I was now checking Twitter every day, I also started following more accounts, engaging in conversations etc – and never left.

Being part of the (academic) community on Twitter has been pretty awesome. From excellent advice about applying for jobs, to thoughtful threads about academic culture, to cat pictures (#academicswithcats), there’s always something to motivate me or cheer me up. Through Twitter I found many friends, role models, and from time to time, even people who were somehow inspired by me. I cannot stress how essential this has been in times of existential crises almost inevitably associated with being a postdoc.

 

7. Blogging

I had a blog on and off during my PhD (see My relationship with blogging), but I didn’t really dare to write anything, let alone tell other people that I have a blog. I had a blog, but I wasn’t blogging.

And that’s too bad. Because since I really started writing and sharing posts (although I still find I’m often outside my comfort zone), lots of interesting things happened. Next to improving my writing and getting me invitations to give talks, blogging has given me a bigger sense of purpose. Related to the Twitter point above, this has been essential for dealing with setbacks.

 

I hope these are useful whether you are doing a PhD or are already done – it’s not too late to start! If you have any other advice you’d like to share with others, please leave a comment below!

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!

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