A System and Software Engineering master's programme alumnus, PhD student from the HSE Faculty of Computer Science visited Broad Institute of MIT and Harvard

Nikita is a graduate of the HSE master’s program in “System and Software Engineering”, who currently does PhD program at the Faculty of Computer Science. He conducts research under joint supervision of Attila Kertesz-Farkas (Higher School of Economics, Moscow) and Peter Horvath (Biological Research Center of Hungarian Academy of Sciences, Hungary, Szeged). The research field is applied machine learning for analysis of biological images. Since he also works at the Biological Research Centre, Nikita spends half time in Szeged and half time in Moscow.

About Broad Institute and how Nikita got there 

Broad Institute of MIT and Harvard is located in Cambridge, Massachusetts. The research activities of the institute are related to biology and medicine. Besides, it has departments with researchers who develop the tools to conduct research. I was in one of these departments – Imaging Platform.

Peter Horvath’s group (BIOMAG) and Imaging Platform already had another collaborative project and another PhD student have got there), additionally there was an idea for a new project too. That is how I ended up participating in the program. 

Preparation

I was able to receive some financial support. eCOST has different actions which are funded. My short-term scientific mission was related to action CA15124 (Network of European Bioimage Analysts to advance life science imaging a.k.a. NEUBIAS). To get the funding, I had to get the following set of documents: support letters from both home and host labs, CV, motivation letter and project description. After I sent all the documents, they approved it. The financial support is officially limited to 2500EUR and you have to describe the expenses, which are usually only transport and housing. 

To get to USA I had to receive J1 short-term scholar visa. As it was my first visit to the US, I had to go through an interview. Eventually my passport came back on the next day after the interview and finally I could buy tickets and book accommodation. It was not hard and took about 2-3 days to collect all the documents. However, it was a very nervous time for me, because I wanted to go, but I did not have any guarantee that the visa will be granted. Additionally, the tickets are quite expensive if you buy them just before the flight. 

Eventually it all went well and I received the visa. Right after I booked a room via AirBnB. My options were quite limited, because the flight was in less than 3 days away. Luckily, I found the room and we did all negotiations with the host very quickly. The house was located in Dorchester, a relatively cheap district, but it also has some cons like the commuting time (it took about 50 minutes to get to Broad) and it was a little bit creepy, especially after sunset. Still, the host was very helpful and kind person, so my time there was fine. 

I lived with three people: a programmer from Brazil, a person from the Netherlands, who was doing an internship in Massachusetts General Hospital, and a guy from Vietnam, whose mother is actually from Russia. We did not have time to chat, because all of us were coming home quite late. 

On the project

Like I mentioned before, I was in the Imaging Platform group, which is led by Anne Carpenter. This group is famous for developing a tool CellProfiler, which is widely known among biologists working with images. Besides that, this group has quite a lot papers in high impact journals.

My project was in applied machine learning – I had to train a model for cell segmentation and do preliminary data analysis of the image datasets we had. I hope that this work will result in a good publication someday. 

I still did contact both my supervisors, with Peter mostly about the progress organization, and Attila for advice in machine learning part. People from the group were also very helpful and it was exciting to get advice from the experienced researchers. I am truly grateful for all their help. 

Experience

First two-three weeks out of eight, I felt uncomfortable as USA differs from Europe. I felt homesick. Then it has become better, but still I felt a bit strange all the way. 

I did submit a report about my STSM, and on the same day after I did the submission I got much better results, that was a strange coincidence. 

It was an inspiring experience. Broad has different events about biology and medicine, so I was visiting the most interesting for me. In addition, MIT is located next to Broad and it is easy to get inside (they don’t ask IDs for entrance), so I was visiting some bioinformatics and machine learning seminars there. Harvard is also nearby; I did visit its museum for a public talk about viruses. Cambridge is a great place to see widely known researchers and attend their lectures\seminars. 

I did visit New York twice for weekends, it takes only 4 hours to get there from Boston and I did go to Yale University campus (New Haven, about 2 hours by bus).