Year in review: third year as a PhD student

As I mentioned before, it’s important to keep track of your successes and disapointments. Since I do have a list of sorts, I decided to share my summary of 2013 here.

Writing

2013 was definitely a year of journal papers. Or at least, of long overdue journal paper submissions. Here are the totals! I submitted four times in total (one paper twice, and two papers once). Two of these were rejections, one “revise and resubmit” and one still under review. So, 2014 probably will be a year of journal paper resubmissions.

Reviewing

Next to paper writing, there was also paper reviewing. In the beginning of last year, I was getting worried that I was not invited for reviews, but this worry turned out to be unfounded. I guess this goes together with submitting journal papers (and getting into the system) and meeting more people, who have more reviews than you, but are also more busy. I want to believe in review-karma: by writing good reviews, I hope to get good reviews. By good, I mean objective and constructive, not necessarily an “accept”.

Funding

2013 was also a year in which I tried to apply for scholarships to finance my conference visits and the trip to Tuebingen. For the second time (the first time being in 2012), I did not get the Anita Borg scholarship. I did get the ACM-W / Microsoft Research grant to go to a conference in China, which was awesome! The application that I spent quite a lot of time on, for the short-term fellowship from EMBO to go to Tuebingen, unfortunately got rejected (after I returned from Tuebingen already). However, I was able to get some financial support through my university, which was not a competitive application, but very helpful.

Research visit

And of course, 2013 was the year I went on a research visit, for which I have not (yet?) been able to write an overview. In short, the three months went by really fast and I had a great time. What everybody says about research visits is true. It is really helpful to experience a different place and get an idea of how people do research there. I think it’s a must for all PhD students, especially from smaller labs. It probably doesn’t even need to be a lab in a different country to get an impression of “how things are done” and to pick up useful research skills. I already have my next short visit planned, what about you? Did you / will you do a research visit during your PhD?

On recording your progress

It’s been almost a year since I started to blog alongside my PhD. I’m not sure whether I mentioned this a year ago, but my initial goal was to write something every week, which quickly deteriorated into writing something every month. With this post, I have been able to keep the latter promise up.

Although I had many moments of “oh, this is something I could write a post about!”, only few of them actually made their way from my thoughts into a digital version. The main reasons for this are, I think:

– too little practice: I really do find it difficult to write something that’s not directly about my research

– too little privacy: there are some issues I would not want to discuss online because my name is linked to my blog and I don’t want my opinions to always be “out there” somewhere. Many of the blogs I find very interesting (not just the ones that are linked on this page) are actually blogs that discuss such issues, and for 95%* these are anonymous.
* I initially wrote 95\% which amused me quite a lot.

– too little expertise: I like posts which contain advice on how to do something better, such as never worrying about poster transport again. The truth is, however, that there are not a lot of things I feel I’m more knowledgeable about than other researchers with blogs.

– too little information: I am, of course, knowledgeable about what I do on a daily basis (submitted this, got rejected for that). Of course, this is mostly relevant to me and not to readers in general. I am aware this is my blog and I can post whatever I like, but I am less motivated to spend time writing something that is not helpful to others. Also, I

What I recently realized is that I would have enjoyed to have more of these “progress” posts, just for myself. In my first attempt at blogging, I wrote about how I submitted my first paper and how a few months later, I got the email that started with, “We are pleased to inform you…”. Or about how I reviewed the paper for the first time, and it turned out to be horrible. It’s nice to remember how I felt then, what my goals were, and how I generally thought about research.

My advice (this is actually a helpful post!) if you are a PhD student: write your successes and disappointments down somewhere. Not necessarily in a blog. Maybe it’s even better if it’s not a blog, you might spend less time worrying about how to write it down, and who is going to read it. But sometime later, you will enjoy reading about these experiences, and what they tell you about your progress. Happy writing!

How to print your posters on fabric

The Problem

Probably all PhD students face this problem in their career: the poster presentation, and bringing the poster with you to the conference. This usually means you need one of those poster tubes to keep your poster all neat until the poster session. Not too bad if you are going to a local conference, but more annoying when you are going to, say, Japan, where I attended the International Conference on Pattern Recognition in 2012.

poster

I was determined to go to Japan with just a carry-on bag, something I have never attempted on trips longer than 3 days. Of course, I would also have a “personal item”: my regular bag for my laptop and valuables. I really, really did not want to add an extra piece of luggage (the poster tube) to the list of the things I had to bring with me. So I decided to look for a solution: posters that would fit into my carry-on!

The solution

For paper, this would mean either a very small poster, a poster with fold lines, or a poster consisting of several small parts. Neither of these seemed very appealing, so my material of choice became fabric. After some searching, I settled on this product, in particular the “vlaggendoek” or “flag sheet” variety. This material weights just 115 grams for 1m2, which is conveniently almost the same size as an A0 (841mm × 1189mm). Printing + delivery costs just over 20 euros, which is actually cheaper than an A0 paper poster with a plastic coating. That’s not all: apparently the material is fire retardant, because you never know when fire could break out at a conference.

But the best thing of all? You can fold it and it still looks great when you unfold it! Here are my two posters folded a few times:
poster folded

These did not only fit into my carry on, they even fit into my purse (and made a great padding for my mini laptop).

I received a lot of compliments (about the content too of course 😉 ) and heard a lot of  “I should have known this earlier!” during the poster sessions. So this is me, telling you: print your conference posters on fabric! If you are in the Netherlands, you are welcome to stop by to see the real thing.


Where else to get it

France: Easyflyer (thanks to @cazencott!)

Belgium: UniversityPress (thanks to @dan_marinazzo!)

Germany: Diedruckerej (thanks to @chrshmmmr

UK: SciencePosters (thanks to @IAugenstein!)

US: Spoonflower (thanks to @jengolbeck!) and Postersmith (thanks to @astent!)

If you know of any more companies not in these countries, please let me know (comment below or via Twitter) and I’ll add it to the list! As of July 2017, I’m still updating the list.

 

Bonus

You can get your textile poster repurposed into a piece of clothing or accessory at REpost Science. See my newest blog post about this.

 

 

 

 

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 🙂

Year in review: second year as a PhD student

This post originally appeared on my previous blog.

After my one-year evaluation, the first thing I did was sign up for a course on presentation skills. To be honest, I hesitated a bit at first, but I started hearing quite a few good things about Art of Presenting Science, so I decided to see for myself what that was all about. I really, really loved it! I can’t really summarize my experiences in a few sentences, so perhaps I will dedicate a whole post to this.  I tried to put a few of the things I learned to the test when presenting my work at the meeting of the NVPHBV (Dutch Society for Pattern Recognition and Image Processing), and at the Benelearn conference in Gent, Belgium.

As for research, I was pursuing several directions that are relevant to Multiple Instance Learning, learning with dissimilarities, or both.  A few of these ideas resulted in submissions to conferences, while others were abandoned after a while. Perhaps “abandoned” is not the correct word to describe the situation, and “on the shelf” would be better.  The ideas are still very interesting, but at the time I did not have enough insight to turn them into something that could be published. I hope that I will have more luck with this in 2013 🙂

In the summer it was time to take a break from my own research, and learn a lot about what others are doing at the Machine Learning Summer School in Santa Cruz, California in the US. The summer school consisted of two weeks of lectures from people from academia and from industry. The proximity to Silicon Valley ensured a lot of interesting talks by Google, Facebook and other companies that have a lot of data and therefore do a lot of machine learning. Next to all the talks, it was a great experience to meet other researchers from all of the world and compare notes on everything from doing a PhD to making tacos. I hope we will meet again!

mlss

As if that wasn’t enough traveling, I received the decisions on two papers that were submitted a few months ago. Both were accepted as poster presentations: “Does one rotten apple spoil the whole barrel” at the International Conference on Pattern Recognition (ICPR), and “Class-Dependent Bag Dissimilarities for Multiple Instance Learning” at the Structural, Syntactic and Statistical Pattern Recognition (S+SSPR) workshop.  S+SSPR was held in Hiroshima, and ICPR was held in Tsukuba, close to Tokyo. With an extra day to recover from jetlag and a few days (because three weeks in the US aren’t cheap) for sightseeing, this meant a two-week trip to Japan. One of my posters in action:

dscf7148

I enjoyed both conferences although they were completely different from each other. S+SSPR was very small, which allowed informal discussions more often and attending a lot of the talks. I also noticed the same type of close community (but with a different subset of researchers) that I saw at Multiple Classifier Systems a year earlier. ICPR was very big, which was a new experience for me. The program booklet was as large as the proceedings of some conferences! Therefore it was quite difficult to choose which talks to attend. I found out that often, my first impression (such as “this is relevant to my research” or “I won’t understand this at all”) was wrong.  In fact, I was pleasantly surprised by a few talks about unrelated topics, but given by a great presenter. There is still a lot to learn for me there.

Although I thought I could deal with time differences pretty well, I did have a few sleepless nights in Japan. On one of these nights, I had an idea about the relationship of my own work to a quite successful MIL classifier. Who wouldn’t get inspired if you are surrounded by wonderful things like this:

dscf7051

dscf7115

 

Instead of scribbling the idea down with a few words, arrows etc, which is what I usually do, I actually started writing the paper. I didn’t get very far while I was in Japan, but I did discuss the idea and let it develop. After the decision to made to submit a paper to Multiple Classifier Systems 2013 (I admit, I loved MCS 2011 so much I just couldn’t resist), the whole process of writing and submitting the paper cost me about a month. Perhaps that might be long for some people, but for me it was definitely a record. I’m also very happy with the process, so perhaps I will try this more often (starting to write a paper as soon as the idea is there).

 

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