Short Report by Karen Pu: Using large language models to automate optimizing thermal stability in protein design (May-August 2023)
During my stay in Leipzig, I worked under Felipe Engleberger to explore the potential for Large Language Models (LLMs) to answer scientific questions. Knowing that LLMs have created such an impact on everyday life through technologies such as ChatGPT, I was excited to contribute towards expanding their function to fulfill scientific tasks, yet like all research questions, executing is much easier said than done. To begin this endeavor, we focused on a specific task–exploring if we could empower a chat agent to find mutations to optimize the thermal stability of a protein, a common question in protein design. I was pretty new to the field of artificial intelligence; thus, I started off reading through papers and playing around with code. As I explored ways to overcome limitations that made LLMs unsuitable for scientific purposes, I learned so much in both the fields of biochemistry and software engineering. Translating important chemistry knowledge and tools, such as mechanisms in which to evaluate induced mutations, into usable and efficient code truly highlighted the interdisciplinary nature of my project. As a computer science major, I have always known that there were so many ways I could apply my skills–and I believe I have found a meaningful direction through my internship
at Leipzig.
Living in Germany was another learning experience outside of my work in the lab. When I first arrived in Leipzig, I realized that for the first time, I was living in a country where I did not speak the main language or understand the culture. That being said, getting adjusted was a bit of a struggle, but as I found ways to adapt, I began to truly appreciate where I was. I loved the bike-friendly roads and the delicious, fresh (and cheap) bread at a local bakery. I enjoyed walking around the market square with an ice cream in hand or swimming in a local lake. On weekends, I was able to travel to different cities, such as Budapest, Prague, Berlin, Munich, Geneva, and Vienna. From staying in hostels, I was able to meet and adventure around with people from different countries and walks of life; when visiting friends, I would walk around the city and learn about the ins and outs of daily life. I believe that this experience truly opened my eyes to other perspectives and taught me skills and habits that I will take back home.