Defending propositions : introduction

Propositions?

In the Netherlands, along with your thesis you defend a few – let’s say 10 – propositions. Propositions are statements that are “opposable and defendable” and cover a number of topics. The first few are usually about the topic of your thesis, but the others can cover pretty much any topic.
These last few propositions are usually the most interesting, as they resonate with everybody – not just people who are acquainted with your research topic. It is a way to show your personality, by voicing your concerns about a particular topic, or even by slipping in a bit of humor. But apart from being a creative outlet, propositions are also rumored to be difficult to write. In this series of posts I share my experiences with writing propositions, which might give you some inspiration for writing yours.

My propositions

To get started, I present to you my propositions:

propositions
[PDF]

As you can see, propositions 1-4 are about my thesis and pattern recognition in general. Propositions 5-10 are about other topics, but most relate to doing research. It is these propositions that were the most difficult to come up with, but most rewarding to refine into their final form. In the upcoming posts, I plan to share more about a few of these propositions. I will also write about the brainstorming process that I went through, and what I think about this tradition now that it’s all behind me.

While I’m getting the other posts in this series ready, please let me know what you think about propositions. Is it a good tradition? Does it add something to the PhD defense or is it a waste of time? If you are are doing a PhD in the Netherlands, are you thinking about what your propositions might be?

Firsts: reviewing a paper

After a conversation on Twitter about when to start reviewing papers, I decided to post about my own experiences with reviewing, when and how and when I started, and what I wish I would have known in advance / done differently.

I was in my third PhD year that I started wondering about being a reviewer. I heard of another PhD student being asked to review, and got worried why that has not happened to me yet. But shortly afterwards, I was invited for two journals, and then more and more invitations (including more important journals where I have not published) followed, so the worry disappeared. In this post I share some experiences about what helped me with reviewing, and what I could have done better.

Getting invited

  • I discussed the issue with more senior academics, who were already reviewing for a while. They gave me some pointers about how they got started, but they also made a mental note of me being a potential reviewer. Then, if they were an editor, a program committee member, or simply unavailable to review themselves, they could mention my name.
  • I started submitting journal papers, which meant that I had to create accounts with publishers. Editors were then able to link my name to different keywords, even if my own papers were not published yet. In fact, most of the invitations I received were from journals that I had never submitted to, but that shared a publisher with a “submitted-to” journal. In retrospect, I could have created the accounts even before I was ready to submit, and indicated that I was available to review.
  • I maintained an online presence with the page at my university and Google Scholar. My guess is that editors who did not know me personally, would scan these pages to get an idea about my research and experience. Having a blank webpage (with only your name and contact details) might send the wrong message in such a case.

Accepting the invitation

Once I got an invitation, I accepted it! The paper was on the topic of my PhD and the invite gave me a feeling of accomplishment (and relief), so I felt ready to do it. It could also happen that you do not feel ready, for example because it is unusual for PhD students to review papers. My advice is to go for it anyway. Somebody else thought you have the expertise you do it, so don’t listen to the impostor inside you, and give it your best shot! Reviewing taught me a lot about my own writing, so I’m happy I didn’t wait until I was “grown up” to start doing it.

Reviewing

Then it was time for the actual review. I spent quite a lot of time on this, because I was doing the review by myself, and I wanted to make sure I didn’t miss anything. I thought the paper was not very strong, but I felt I couldn’t rely on just my opinion to say that. So, I discussed the approach with my supervisors, who agreed with me.
Then I read a few “how to” guides and started writing what I wanted to be a constructive review. I also went over the reviews I had received for my papers, as both good and bad examples of reviews. This was more insightful than the guides, so in retrospect, I should have asked colleagues for more examples to learn from.

An alternative would have been to ask a supervisor or colleague to go through the review process with me from start to finish. At the time, I probably thought this would be asking too much, but now I feel that many academics would be happy to do this.

Keeping track of reviews

I created a folder called “Reviews” with a subfolder with the name of the journal, and stored the submission and my review of it. This seemed sufficient at the time, as most people listed only the names of the journals on their CV. But it might be a good idea to keep track of what happened to the paper afterwards, should you need that information later.

Update 4th of October 2016: I found an excellent place to keep track of reviews, share reviews and even rate reviews written by others: Publons! I am still in the process of adding reviews to my profile, but you can already check it out here

On choosing to do a PhD

This week I gave a talk at the career event of my former student society for mathematics and computer science students, ‘Christiaan Huygens’ (CH). All the speakers were asked to talk about their work, and the choices they made to get there. As it wasn’t always my goal to do a PhD, I thought it would be good for the students to hear about the doubts that I had. And now, for the purpose of sharing N=1 experiences, I’d like to share these thoughts with a wider audience.

Choices

One of the courses I followed during my masters was Pattern Recognition (IN4085, for the readers from TU Delft). I was immediately sold. It seemed magical that reading licence plates, recognizing faces, or predicting a patient’s diagnosis, were all based on the same underlying principles. I followed all the courses I could find on related topics, and did my graduation project on a pattern recognition topic (here is proof).

I was convinced that my job had to do something with pattern recognition. But, I also wanted to somehow apply all the other skills that I had developed during my student union time. As many of my classmates were choosing consultancy jobs, I was excited to find out that there was something similar there to match both my interests: a data analysis consultancy job at a large company in Amsterdam. Note that this was 2010, and nobody was hiring “data scientists” yet, at least in the Netherlands.

Everything was going really well with that company. I had visited them to find out more about their projects and meet the team. I really loved the new environment, and I was convinced I would be hired after an interview. Shortly afterwards, an opportunity to do a PhD in Delft came up. That was also an environment that I loved, but it was entirely different from the job in Amsterdam. It was safe and familiar. After all, I thought that during my MSc project I had already figured out what research was about (cough cough). Fueled by the belief that you should always do new and challenging things, I felt that a PhD would be seen as an inferior choice.

Doubts

But, doubts also started to creep in. I could not define them fully at the time, but now I am quite sure the doubts were: (i) I wasn’t sure I would be challenged enough by the technical challenges of the job in Amsterdam and (ii) I thought I would be challenged too much socially — always looking professional, always interacting with people. All things that I enjoy, but perhaps not every day, and not coupled with a long commute.

Perhaps my biggest problem was that at the company, it would be part of my job to oversell things — make things seem more impressive than they are to clients, and come up with convincing arguments on the spot. This ability was considered very valuable among my classmates, and I imagine quite sought after by companies. I of course felt honored by the company’s belief I had this ability, because it wasn’t something that came to me naturally. So while I was excited and challenged by the prospect of developing this ability, it also felt like I would be betraying myself a little bit.

Best advice I received

One thing that helped me in my decision is a conversation I had with a former student. He had just finished his PhD and was switching to an industry job. The advice was to

  • compare concrete opportunities (rather than PhD vs not PhD)
  • consider the people I would work with and the daily tasks I would have to do
  • whether I could be myself, and how the position would fit in with the rest of my life

This cleared things up for me, and once I had accepted the PhD position, it felt like a huge weight off my shoulders.

I didn’t regret my decision for a second afterwards. I had a great time during my PhD because of the people that I worked with, not only inside the lab, but also other researchers that I met at conferences. I discovered I was very wrong about knowing what research is about! There are new, exciting and challenging things in my job every day, but challenging in a way that is meaningful to me.

I also had quite a lot of freedom, both in the ideas I pursued and in managing my time. I was in the office during regular work hours, but I appreciated being able to take a day off, go on holiday, or work at home if I wasn’t having the best day. I felt that I was being valued for my ideas, rather than for showing up. And isn’t being valued one of the most important components for job satisfaction?

Keep in mind

That is not to say that you should always choose a PhD when in a similar situation. There are huge differences in PhD positions as well! Not all researchers are nice people, and not all projects offer the same freedom that I had. I hope that this strategy — considering concrete opportunities, and staying true to yourself — should help you with the answer.

Why you should post preprints on arXiV

Recently on Twitter I saw a lot of discussions about preprints, such as under the #ASAPBio hashtag, which originated in the biology community. My guess is that preprints are more or less common in different fields, and I thought it was normal for Computer Science to do it, so I couldn’t contribute anything to the topic. But I’ve encountered some doubts when I encouraged other CS students to upload their work to arXiV, so I thought I’d share my N=1 experience with preprints.

Long story short, I spent a good part of 2013 writing journal papers. I submitted three of them that year, and directly uploaded the submitted versions on arXiV. You can see my page on arXiV here.

I spent 2014 revising these papers. One paper was accepted in 2014, and two others only in 2015, when I was already a postdoc. One of the accepted papers is still in press, even though it is already 2016. I imagine it will be three years (!) between my initial submission — that really isn’t that different from the revised version — and the published version. And this is in Computer Science, a fast-moving field!

As a PhD student / postdoc / aspiring researcher, you can’t really afford such a time lag. And that is where preprints have been immensely helpful to me in different ways:

  • Two of the papers were based on earlier conference papers. When I was discussing that work with other researchers (at conferences, via email), I could send them the preprint, which contained more detailed results.
  • The third paper (a type of survey) was completely new, and I was a bit scared that somebody would publish something similar before me. The preprint was actually a way to assure myself that it was now documented that I came up with the idea. Again, I discussed this work with other researchers while it was already in arXiV, and even got some valuable comments, which helped me a lot when revising the paper.
  • The preprints were cited (mostly by myself, but also by other researchers). After publication, I merged each preprint with the published version in Google Scholar. I don’t really have a lot of citations, but I would have had even less if the papers only became available in 2015 instead of 2013.
  • I didn’t apply for jobs while I had any unpublished preprints, but if this was the case, I could put the preprints on my CV, which is more informative than simply listing the paper title with the comment “manuscripts in preparation”.
  • Most journals allow this! You can check on this website what your journal’s policy is

If you are a student in Computer Science (or anything, really) and you are doubting about uploading a preprint of your recent work, I hope this might change your opinion a little bit.

Firsts: preparing for a lecture, part 2

“>Here I started preparing for my first lecture and describing my experiences. Now that the lecture is over, I have a few more things to share about the whole process.

In the end, I think I spent 20 hours preparing (not 30 as I estimated previously). At some point I felt I was satisfied with my story and I didn’t feel I could change anything until actually trying it out. In terms of the “how to”, I found a teaching course on Blackboard, and looked through the first teaching lesson. There are some useful tips there on keeping the attention level of the students high, and on structuring the lecture, such as providing summaries. With this in mind, I revised my slides one final time, for a total of around 30 slides for each 45 minute lecture.

During the lecture, a few things went differently than I originally planned. For instance, I included short summary/overview slides for transitions between different topics. However, every time I felt that I already explained this twice, so I did not put too much emphasis on it. In the end, it turns out that I should have done it anyway, against my intuition :). For other slides, I realized that I could have explained something in a different way, or linked the topic more to something students are already familiar with. I received some helpful tips about this from my supervisor, so I hope I can apply these in the future.

Another thing that didn’t go exactly as planned was the timing. I am very happy that I was using the presenter mode in Powerpoint where you can see the time and your notes on the laptop screen. I was too involved with the lecture to actually look at my notes, but the time was very helpful. I realized that I started too quickly, so later on in the lecture I tried to go a little bit slower. In the end, both lectures were finished in under 45 minutes.

Overall, I think the lecture was quite a nice experience! I was not too nervous about it, and although there were some silences (such as after a “Are there any questions about this”?), there was also student participation after some of my other questions and examples. That was very nice, especially because students started thinking of how to apply the method to their own PhD research. And that’s what the course is all about!

Firsts: moving for an internship

Exactly three weeks ago I got on a train to Tuebingen, Germany, and right now I feel I can say that I’m settled in, which means it’s time for a post.

One of my goals when coming here was to concentrate on the project that I am here for. Therefore I wanted to spend as little time as possible on “settling in”, and although I can’t say I was 100% successful, I learned a few things that might be useful when moving to a different country (even if it’s just from the Netherlands to Germany).

Luckily, I was able to arrange a room beforehand, and the room was furnished. I assumed I only needed to get bed sheets, so I ordered those at IKEA and had them delivered to the house before I arrived.  However, “furnished” does not mean “you have everything you need”. Here are a few things I did not really think about, and really missed in my new room:

– A sofa. A bed (though very comfortable) is just not exactly right if you want to read, watch a movie or relax without falling asleep.

– A coffee table. For the laptop that is getting too warm, or food and drinks to go with the movie.

– A coat rack and hangers. I’m not too organized when it comes to my closet, but hanging things up is easier than folding, and a few items (coat, bath robe) just don’t belong on a shelf.

– An electric kettle and a coffee machine. Tea and coffee are basic necessities and specialized tools definitely beat heating up water in a pot on the stove or in the microwave.

– Laundry “accessories”. There is a washing machine in the building, but laundry needs to be stored and dried somewhere as well.

About half of these things I bought second-hand (through Facebook groups or at flea markets), the other half from convenience stores. Now life is more comfortable 🙂 A few other things that I arranged as soon as possible, and that have been very helpful, are:

– A prepaid SIM card with internet. I’m using with my dual SIM phone. I would recommend Alditalk (great value for money), but not so much the phone (dual SIM is great, but it’s quite slow compared to my deceased HTC Desire S).

– A bank account. I did not really want to get one for the few months that I’m here, but the German bank card-operated washing machines thought otherwise.

– A bus pass. I only need to worry about which bus I get and where to get off, not about having the right amount of fare.

– A bike! For all the times that a bus is not that convenient, AND it feels just a bit more like the Netherlands now 🙂

 

Firsts: writing a grant proposal

Despite my previous post about having a whole month to myself to write a journal paper, things went a little bit differently. A fellow PhD student pointed out these short-term fellowships and I decided it would not hurt to try to apply, so I could finance the second half of my visit to the Max Planck Institute in Tübingen. Because I already had a few scholarship applications lying around (such as for the Anita Borg scholarship, which I applied for twice, unsuccessfully), I thought a new application would not cost me more than 2 days. In the end, I spent around 2 weeks working on the new application and neglecting my journal paper, but I still believe it was time well-spent!

One thing that was different about this application is that it was not focused on me, but on the project. Of course, I already had an idea about what I would be working on at the MPI and how that fits together with my PhD topic. What I underestimated, is that I suddenly had to explain all of these machine learning problems to people with a different background – I assume molecular biology, as that is the core subject of the organization providing the fellowships.

What really helped me with writing, was a successful proposal, which was on a different topic, for a different fellowship, from a different organization, kindly provided to me by a colleague. It was a good example of HOW to write for a different audience, rather than WHAT exactly to write about. Here are some of my findings:

  • Don’t assume a term that you use every day is obvious to everybody else. Provide a short explanation and an example. If possible, use pictures in your explanation.
  • Provide references, even if something is common knowledge in your field.
  • Use short, clear sentences in the active voice (“We will conduct experiments…” rather than “Experiments will be conducted…”), here is a good post on how to do this.
  • Avoid words that make you sound unsure, such as “probably”.
  • Include questions which your project will address, such as “What is the cause of X?” or “Is it possible to do Y?”
  • Don’t be afraid to use bullet points for lists, this is probably easier to read than a paragraph of text that does not really fit together.
  • Be explicit about how your previous work is going to be helpful in this project, it might not be obvious to the reviewer that your list of publications is related to the research topic.
  • Ask others (especially people outside your lab) to read your proposal.
  • If possible, use examples (both successful and unsuccessful) of other proposals.
  • Don’t underestimate the time that you will need for writing 😉

I will only get the results of my application in a few months, but I hope these tips can be helpful to other PhD students that are in a similar situation.

Update: the proposal was not funded, but I received funding for my internship from another source, so it was a good experience overall

Firsts: preparing for a lecture, part 1

I’m very proud of it and very scared at the same time – next week I’m going to give a lecture for the first time. The lecture is a part of the Advanced Pattern Recognition course for PhD students and my own lecture will be about the dissimilarity representation and multiple instance learning – topics I should be familiar with 🙂

Right now I’m spending a lot of time in preparing for the lecture. I’m guessing that 30 hours will be a good estimate for how much time I will spend in total. Right now I will try to explain my progress and how many of these hours I am spending where.

I spent an hour or two searching for information on how to prepare your first lecture. I found helpful tips here and here. The main messages for me is: pick a few core topics and explain them well, rather than skipping over all the possibilities.

With that in mind, I started thinking about the actual content. Although the topic is very related to what I’m doing in my PhD, I want to talk more about the general techniques rather than the specific parts that I am doing. Therefore, I could not use the typical structure of my conference presentations. I started out with a mind map (or at least, a bunch of words with arrows between them) of both topics to see what exactly I would need to cover. In my head, I was already preparing the connections between different topics and thinking of nice examples, so in the end, this process costed me about 2 hours.

Then I looked at which topics I feel comfortable explaining (most related to my own research), and which topics I don’t have experience with / haven’t tried explaining to others. For instance, with a dissimilarity representation, there are two main possibilities to improve upon nearest neighbor classification: embedding the dissimilarities, or training a classifier in the dissimilarity space. In my research, I only do the latter, and although I understand the concept behind embedding, I don’t feel as comfortable with it. Yesterday I spent most of the day reading about it and at the same time trying to revise last year’s slides so I could actually use them in my own explanation. This turned out very time-intensive (+/- 7 hours), but also very helpful.

I still need to prepare the slides for my more “comfortable” topics, revise the whole story and practice. I’m not really into practicing the whole thing before presentations, but here I’m especially worried about the timing, because I have never talked for 1.5 hours before. Also, as my lecture is only on the fourth day of the course, I plan to attend the other lectures and see how the experienced people are doing it. So, probably I will revise a few things after that as well.

The last, somewhat more optional part, is to go over the exercises that “go” with my lecture. Because the content and slides that I’m using changed from the previous years, I have to check whether the exercises are still useful, and update them if necessary. I’m actually very looking forward to this, but I’m afraid I won’t have the time to come up with my own exercises, test the code, etc, so I might have to leave that for next time 🙂

To be continued!

Firsts: visiting a lab for an internship

Last week I visited the Machine Learning & Computational Biology group in Tuebingen. It’s difficult to summarize everything, but Tuebingen is a nice city, the institute is a great place to do research, and there are a lot of friendly people there! Therefore I am looking forward to my longer (few months) visit in the fall of 2013 🙂

At the group, I gave a presentation about my work, attended other talks, and discussed the project that I would be working on. The project is still being defined, but it is probably involve classifying brain data, and in particular, the connections in these brains. For instance, it could be the case that healthy people have different connections in their brains, than people suffering from neurological diseases. I hope to find out more about this very soon.

I also have to find out more about living in Tuebingen, and getting financial support to do so. So far, most grants seem to be for MSc students, PhD students who do not get any salary (but they are also supposed to be in the Netherlands, where PhD students DO get a salary… confusing), or more senior researchers. There are a few things I have to investigate further, so I hope something will come up :). It’s amazing (and unfortunate) how much time this search is costing me, though.

Another thing to think about is learning German. I don’t think it’s really necessary for a short visit, but I enjoy learning languages and I’m curious how quickly I could pick it up. There are no courses in Delft (they do have Chinese though, how awesome is that!), but there is a language exchange program. You pair up with somebody who can teach you a language, and who can learn a different language from you. I’m going to try that, and maybe also just start by myself. There must be an app for it!

Let me know if you have any experiences with exchange scholarships for PhD students, or with learning German 🙂

Writing papers online with ShareLateX

I’m working on a paper together with a PhD student who is technically in my lab, but geographically in Cuba. For some reason, neither SVN nor Dropbox were working, and I was afraid we would have to resort to emailing the paper to each other (the horror!). Then during lunch I thought that we could just use GoogleDocs for the LateX file, or maybe that GoogleDocs even supported LateX. It’s such a simple idea somebody had to already have thought about this!

And indeed, ShareLateX has! You can sign up and create LateX projects and invite others to collaborate with you. Then you have your main file, any other files you want to add, and a button that compiles the .tex file into .pdf (and you can even choose whether you want the latex or pdftex version).

Again, the idea might seem very simple, but I’m still somewhat in awe… You can work on the same LateX file real-time, without waiting for somebody to save, commit or upload a new version. This is very motivating because you see the paper changing so quickly. It is also much easier to decide things together, such as adding that new section, because you already see how it would change the paper. Last but not least, you are all using the same compiler, so you can’t mess up the tex file for each other 🙂

There is  a down side, of course. The free version only supports 2 collaborators and there is no version control. As soon as you want an upgrade, you get the “Collaborator” account which allows 10 collaborators per project but also costs you $15 a month. Not a lot if the only thing you do is write papers with people overseas, but too much if that only happens once or twice a year. I only hope that universities realize how service is great for the researchers’ productivity, and offer it to employees free of charge 🙂

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