From studies in Brno to a postdoc position at Harvard! Be inspired by the story of David Kouril

Radka Grace for fi.muni.cz

David Kouřil, a former student of the Faculty of Computer Science at Masaryk University, gave us an exclusive interview. David shared with us bits and pieces of his academic journey not only at Harvard, his research activities and added some tips on how other students can achieve the same. Let his story be an inspiration to you.

Hello David, to start the interview, we'd love to have you briefly introduce yourself.

My name is David Kouřil and my area of research is data visualization. I am currently working as a Postdoctoral Research Fellow at Harvard Medical School in Boston, USA.

I was born in Zlín. At FI MU I studied the Bachelor's program "Computer Graphics and Digital Image Processing" and the follow-up Master's program "Computer Graphics". Thanks to the Erasmus exchange program I did my thesis in cooperation with TU Wien in Vienna, where I also did my PhD.

That sounds very interesting. Do you continue to collaborate with your "alma mater" - FI? If so, what are you working on now and will you continue to work on during your time at Harvard?

I returned to FI from Vienna for two years as a postdoc. It was a bit of a coincidence. I hadn't planned to continue in the academy. The postdoc at FI, in Bára Kozlíková's lab, was a time for me to recover from a demanding PhD. It also gave me the freedom to find my own direction in research.

Perhaps an interesting side note: I almost didn't get this postdoc position. I was ranked third for two open positions, but someone above me declined the offer. :)

We've been working on visualizing chromatin structures in 3D here. In 3D we mainly study molecules such as proteins (note: Bára Kozlíková has many years of experience in this at FI), but chromatin is specific in its size and dynamics, which makes it impossible to look at this structure directly. Therefore, this area is an active research in biology, which makes it attractive for visualization.

When did you first think of going abroad to study as part of your studies and why?

During my childhood, I spent holidays with my parents in different parts of the country. It was not until I was 23 that I went outside the Czech Republic for the first time. During my studies I was very tempted to stay abroad. I knew about the Erasmus programme, and I knew people who had gone somewhere. Still, I vividly remember that it was difficult for me to commit and apply for the programme.

In the end, thanks to Bára Kozlíková, I managed to apply. I wrote to Bára about what I was interested in and that I would like to go somewhere to work on my thesis. She was on a trip to Vienna at the time (at TU Wien), where she liked the visualization group there, so she pushed me a bit. (smile)

When did you decide to continue further in academia and do more in-depth research?

It was definitely a gradual process. I certainly wasn't a student who knew from primary school that I wanted to do research or be a professor (I don't want that now either :)). It's more that technological development in computer science has always been closely linked to academia. My primary motivation was Pixar movies. They made me aware that there was research within computer graphics, and that this research was happening at the intersection of academia and industry. And then it's just a matter of going in a direction, finding other directions along the way, and gradually specializing.

And you've chosen your specialization very well. Please describe your research activities in more detail, what do you do in particular?

I like to use programming and computer graphics for purposes other than entertainment. So I got into data visualization through interactive art, and so-called creative coding. My specialty has become biological data, which describes the environment of molecular and cell biology. Due to the fact that these are environments and processes that take place on a scale from nanometer to micrometer (which humans are not able to observe with the naked eye), it is sometimes hard to get a proper idea of what is really happening in the cell. And this is where visualization is a very useful tool. It helps us to make sense of measured and often large data, to piece together information from different experiments and to present hypotheses. I am specifically interested in interactive visualization of 3D spatial data, which requires the skill of programming graphical applications in real-time computer graphics.

What was your educational journey from graduating from MU to getting accepted to Harvard? We know that you did your PhD in Vienna and won major awards for your PhD thesis, IEEE VIS 2018 and EuroVis Best PhD Award 2022, congratulations and please tell us about that as well.

That's right, I was already involved in research projects at TU Wien while completing my Master's degree and the PhD in Vienna was a natural progression.

The PhD was a chapter in itself, on the one hand it was a challenging environment and a lot of uncertainties: you don't know if you are working on the right projects, if you will be able to publish papers and if you will be able to finish the PhD before the funding in the project runs out. Somewhere in the middle I had a big crisis and almost quit. Thanks to my supervisor, Ivan Viola, this did not happen, for which I am now glad.

The other side of the coin is that my PhD has put me in contact with the absolute top of our field, I have had the opportunity to travel the world through conferences, meet great people, some of whom have become friends for life. Most importantly, I learned that if I want to move on, I have to go outside my comfort zone. Where I'm the least experienced person in the room who doesn't really know what they're doing compared to others. And staying open to everything in that situation, soaking it all in like a sponge and learning as much as I can.

The award for the best PhD dissertation at the EuroVis conference, then, was kind of the final stamp and confirmation that I did a good job, even if it didn't seem like it most of the time.

What was your PhD research and are you continuing to work on it at Harvard or is your current research different and what is it? How long will you be doing research at Harvard?

My PhD thesis focused on how visualization can be used to communicate biological structures and processes to people with no prior deep knowledge of biology. This is called "science outreach" and involves all sorts of media - illustrations, animations, even computer games; designed to bring science to the general public. My articles mainly illustrated how the different "components" fit together and how they form complexes, for example viruses occupying several scales.

At Harvard, my focus is slightly different. I work more on developing visualization tools for biologists themselves. Specifically, I'll be working with genomic data. One of the important questions that biologists have been trying to answer for decades is the arrangement of genetic material in the cell. To perform all the functions of this material, we focus on its size relative to a small space and how to rearrange it efficiently. There are experiments that are able to indicate the properties of this arrangement, but the specific method is still unclear. Visualization can help in consolidating current knowledge and generating new hypotheses.

My position is specifically at Harvard Medical School, within the Department of Biomedical Informatics. Perhaps the biggest difference is just that it is not a pure informatics "faculty", but an institution directly involved in biomedical research. This means that I get to be close to the actual applications of our visualization techniques and tools, since biologists sit a few desks, or at most a few rooms, away. Boston is a big center for biomedical research.

Your research in IT has led you to other fields - what are those fields/areas and what is and has that been like for you? What has been the most difficult? And is there anything that fascinates you?

This is perhaps the specificity of working in such a multidisciplinary field as data visualization: it is a very versatile skill that one can apply in any field. For me, of course, it's biology.

The hardest thing is to find common ground with experts, especially in the beginning, because we are normally talking to experts about topics to which they have devoted at least one PhD, sometimes their entire scientific career. We usually have to catch up in a very short time. The important thing is to get to grips with the topic and learn at least the minimum to see where we can have the biggest positive impact with the technology.

And that's the most fascinating part of it, you have to keep learning and looking for connections and universal principles. And when it's the worst, we just write a program that makes some part of the job easier or faster for someone.

When did you first get the idea to go to Harvard and what was the admissions process like?

The most challenging part was the actual decision of whether or not to apply for a position. Especially with a name like Harvard. Luckily, I had people around me who were supportive. Especially my wife, who told me that she couldn't look at me anymore in my uncertainty, and to give it a damn try.

Fortunately, I knew roughly what kind of research this group at Harvard was doing. At the time, I was working at MU on a similar, complementary, topic. So I struck up a collaboration and did a little checking on them to see if there was any overlap of interests.

The hiring process was pretty simple: an invited talk to the whole group, then a couple of rounds of interviews with the group members (PhD students and current postdocs), and then one with the PI (principal investigator). Here is perhaps one advantage of the academy: one builds one's reputation by articles and participation in the community, so in a smaller field like data vis almost everyone knows each other. Certainly no one grilled me about coming up with algorithms on a whiteboard.

I got an offer based on interviews. I also got an invitation to come to Boston, which helped a lot. Sometimes you need to see people and a place in person and see if it's the right environment to work and live in.

Being accepted to Harvard is a great opportunity of a lifetime. What were your feelings when you were told the news?

I was more or less happy to have another job. (smiles) It makes me happy that the topics and ideas I have have potential even at this world-class level.

What was the most valuable experience you gained during your earlier studies at FI MUNI and how did it help you in your further academic growth?

To be honest, I found the most useful thing to be my involvement in teaching. Having the opportunity to be on the other side, leading exercises, preparing assignments or evaluating results are all very useful experiences.

Two of my absolute favourite courses were "Introduction to C" (Petr Švenda), where there were several assignments per semester and you had the chance to really immerse yourself in the problem. There I found that I was able to come up with solutions in a bottom-up way. No need to look for tutorials and dozens of materials, just think and figure it out on your own. The Kontr system was a totally great source of adrenaline too!

And then also "GPU Programming" by Jiri Filipovic, which was mainly evaluated based on optimizing a certain algorithm on the GPU, and ranking among other students in the course. Quite ideally, as a student, I would like to have two, maximum 3 courses built on projects, where you can dive deep into the issues, instead of studying right before the exam.

Now a more personal question: How will your personal life change with coming to Harvard? What are you most looking forward to?

The biggest change is, of course, moving away from home. When we lived in Vienna, it was always close. Our days now revolve around our daughter, who was born last year. I don't expect much change in that, just a different environment. And that's what I'm most looking forward to: a new city, new people, new surroundings ready to be explored. It's like the beginning of a computer game where you don't have the whole map uncovered. Also, living near the ocean, even if it's not exactly a swimming resort, is a big draw for me for some reason.

What is your opinion on the importance of international study and experience for personal and professional development? What is your advice for students considering a similar study abroad path?

For me, ideally it would be a necessary part of studying at university. Even within a PhD, there are differences between systems in e.g. Austria, Germany, UK, or the Netherlands, and different research groups do things differently. One learns a lot not only professionally but also personally. It's not for everyone, but at least that way you find out what you want and don't want.

For particularly ambitious students, I would definitely recommend travelling as soon as possible, even during your undergraduate studies, and ideally continuing your studies abroad. If they don't think they can do it, they should believe they can. I recommend always keeping in mind that I'm going somewhere to push me up to the next level. If I have it in my head that I'm already the best at everything and have nothing to learn, there's no reason to go anywhere.

Do you have any tips or advice for current FI MUNI students who would also like to get into a prestigious university?

I certainly wouldn't aim for prestige or the name of the institution. Often that "brand" can be redeemed by other aspects. Also, if I tell myself that my goal is to end up at Harvard, anything else can be seen as a failure.

I once read a book by astronaut Chris Hadfield about his journey towards his goal of becoming an astronaut, even though it was highly unlikely for a Canadian at the time. The part that stuck in my mind was that he would have been happy even if he had spent the rest of his career in whatever position he held along the way. That's what I try to practice as well - not worrying unnecessarily about where I'll end up, but whether I'm currently doing the best I can on the road to some goal.

I think there are a lot of useful people in academia who are able to combine multiple interests and skills. An example from my life: I've always liked drawing as a hobby, but I was never good enough to make it my main focus. I often wondered if I was just wasting my time. But during my PhD it was a great advantage. Through drawing I was able to express ideas visually, and it became part of how I present my work.

And my final piece of advice is, "Don't wait for an opportunity to fall into your lap. Opportunities are waiting for people who ask for them."

Do you have any plans for a future career after graduating from Harvard? Are you thinking of returning to the Czech Republic or staying abroad?

That's hard to say right now. We'll see how much we like Boston and how much we'll miss our family. We saw each other for a long time in Vienna, but my wife and I have to learn German properly. (smile)

Great, so we wish you all the best. Do you agree that we should contact you again in some time (maybe 2 years) and ask how you are doing and how your research is going at Harvard?

Absolutely!

Excellent! We are looking forward to it! Thank you for the nice conversation and your time. We wish you every success and joy in your research activities at Harvard and in your personal life.

If you would like to learn more about David and his research activities, please visit him on one of these pages (note: David has given us permission to publish these pages):