ML and Bio: A Summer in Heidelberg

 

Nandan Thakur (2014 batch, E&I, BITS Goa) shares his experience of summer research in Machine Learning applied to Computational Biology at EMBL in Germany.


 

Q. Give us an overview of the internship- where did you intern? What was the project and its duration?

A. I worked in the Gibson Team (Structural and Computational Biology Unit) of the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany for a period of three months over the Summer of 2018 from July till September-end. My project was in the domain of Machine Learning in Computational Biology. I developed a Binary Classifier using Logistic Regression to predict kinase substrate site phosphorylation (i.e.) to check how confidently can a kinase phosphorylate a particular substrate site. For Non-Biologists reading this, this problem corresponds a Binary Classification Problem with heavily imbalanced datasets.
My Lab is appropriate for students interested in Structural and Computational Biology. The Gibson Team in EMBL, Heidelberg deals with investigations with protein sequences, interactions, and networks.

EMBL
The European Molecular Biology Laboratory campus in Heidelberg, Germany

Q2. How did you find out about the program and how did you go about the application process?

I got really lucky. I got placed in January via on-campus placements. Most of February was spent at home. I formally started searching in March for a summer internship to add some vital experience in my resume. Additionally, wanted to travel and explore some cities outside India. I got really late in applying and that was being reflected, as all machine learning summer school program application dates were either over or I wasn’t eligible (some programs allow only US/Europe undergraduates). I got dejected and stopped searching. Later, via a senior of mine (thanks, Shahnawaz Ahmed!), I found out that a professor in EMBL was looking for someone to work over the summer. After 2-3 Technical Skype Rounds, I finally got the position and opportunity to visit EMBL over the Summer.

“…go with the flow, try something out and if you feel it’s a good opportunity go ahead and grab it.”

Tips for Skype rounds:

  • It’s important to have a good internet connection, so for just a day use 4G, campus internet is always not so reliable.
  • Make sure your CV is up to date and be confident with everything mentioned in your resume. It’s fine if you don’t have a big 2-page resume or big MNC names such as Microsoft/Amazon or Gsoc written in it, Just be confident in yourself and in your resume. You should be able to speak each and every line in your resume for hours.
  • Just be calm and always smile in the interviews, You’ll do great I’m sure!

For those who are looking for summer internships, I’ll suggest you should definitely start with the process in November-December itself. Google stuff; every internship opportunity is mentioned online. One note of advice: always ask seniors, friends or relatives for suggestions – you never know from where you can find help. Lastly, I find a lot of Juniors saying they are not sure whether they like a particular field or not. All I can say for now is go with the flow, try something out and if you feel it’s a good opportunity go ahead and grab it.

EMBL1
The DNA-inspired double helix interior of the EMBL Advanced Training Centre

Q3. How did you select your professor/field? What are the potential applications of your work or future directions of your field?

There wasn’t much of a choice in my case. I always admired the infinite applications of machine learning in all domains, particularly in biological sciences, for good moral reasons which motivated me to pursue my summer internship and delay the joining date of my company. I never was exposed to research before this, but I had completed several machine learning internships in NLP and Data Science Startups. So I found this opportunity a perfect time to get some exposure in research and to check whether my interests align with it for a possibility going for Master’s/ Ph.D. in the future.
Machine Learning and Data Science are some of the hottest topics of the 21st Century and have tons of applications in every field possible.

“Check for Student Trips Facebook pages for budget travels (beware: you’ll find mostly Indians in these)”

Q. How was your experience outside of the work? How was the university and city/country in general? Any survival tips?

EMBL had a really nice environment to work peacefully. Everyone in my team would be helpful. Every Friday evening, there used to be a pizza session too! Everyone was friendly, cheerful and helpful in general with doubts.
Germany is a beautiful place to spend the summers. I would recommend making the most out of one’s own time in Europe and visiting as many places as one can. It was the first time I was visiting Europe and I absolutely fell in love with it. The culture, fresh air (I’m from Delhi), mental peace, polite and friendly personality amongst people are hard to find elsewhere.
I used to visit places over the weekends. Personally being more of a nature lover I’d suggest that people visit lesser-known travel destinations such as Slovenia and Croatia as these are rare places with aesthetically pleasing treks through the forest, waterfalls, mountains, and beaches to take a swim. For city lovers the list of great trips is endless – Berlin and Munich in Germany; Rome, Bologna and Florence in Italy; Paris and Strasbourg in France; Jungfrau, Interlaken, and Basel in Switzerland; Amsterdam in the Netherlands; Mallorca and Barcelona in Spain; Prague in the Czech Republic; Budapest in Hungary; Vienna in Austria. Check for Student Trips Facebook pages for budget travels (beware: you’ll find mostly Indians in these) or if you are more of a solo adventurer, go for cheaper travel options with FlixBus and RyanAir, and book hostels or CouchSurfing for the night.

Well, I didn’t learn or know a single German word before reaching Heidelberg but Google Translator, in the end, saves the day! For survival- definitely, learn how to cook! Carry a lot of Indian food if you are a vegan.

41678503_10211908145723410_913205257964617728_o
Nandan with fellow members of the Gibson Team at his farewell dinner

Q. Did you face any hurdles before or during the internship? How did you overcome them?

Not really. I would suggest that one make visa appointments well in time. At least 2-3 weeks before the date of departure for Schengen countries. During the internship, I was welcomed into the team smoothly and was helped to adapt to the team’s culture. Apart from daily hair-pulling over bugs/errors in the code, I never faced any hurdles during my internship.
A word of advice for juniors: even though you might get rejected from lots, in the end, you only require only one good acceptance which you’ll achieve with hard work and dedication and a bit of luck.

My Lab – https://www.embl.de/research/units/scb/gibson/members/index.php?s_personId=CP-60003209

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