By Katie E. Ismael
Four standout undergraduate engineers from UC San Diego were among the impressive group of students recognized recently by the Computing Research Association (CRA) for their significant contributions to research.
The 2021 CRA Outstanding Undergraduate Researcher Awards named bioinformatics major Bonnie Huang and data science student Raechel Walker as finalists and Computer Science and Engineering (CSE) students Kabir Nagrecha and McKenna Lewis as honorable mentions. All were nominated by faculty from CSE.
Learn more about these students’ research, their CSE faculty mentors and their future plans in the following Q&As.
Bonnie Huang
Bioinformatics
Nominated by: Melissa Gymrek, assistant professor in CSE and UC San Diego School of Medicine
Tell us about some of your research.
Currently, I am an undergraduate researcher in Professor Melissa Gymrek’s lab, where I’ve been developing a novel software tool called SISTR (Selection Inference at Short Tandem Repeats). SISTR analyzes specific short tandem repeat (STR) mutations in the human genome and scores them based on how likely they are to be harmful and cause disease. In our paper, recently published in “Nature,” we applied SISTR to a study of de novo STR mutations in children with autism spectrum disorder and identified which mutations are most likely to be evolutionarily deleterious and contribute to autism risk. Furthermore, I had the opportunity to give a platform presentation on SISTR at the American Society of Human Genetics 2020 Meeting.
*Huang worked with Professor Melissa Gymrek on a paper published in “Nature” that finds tandem repeats, which are also associated with Huntington’s disease, may contribute to Autism Spectrum Disorder.
How has CSE helped you in this work and recognition from CRA?
The CSE classes I have taken at UC San Diego have given me a solid foundation in computer science and bioinformatics and the skills and knowledge I have gained have helped me tremendously in my research. I especially enjoyed Professor Gymrek’s CSE 185 course (Advanced Bioinformatics Lab), which deepened my interest in bioinformatics and genomics. Furthermore, I am very grateful for the opportunity to work on SISTR and be a part of Professor Gymrek’s lab. Her mentorship and support have been invaluable in helping me grow as a researcher.
What are your plans for after graduation?
I plan to go to medical school and become a physician scientist. My goal is to pursue a career in academic medicine, since I am drawn to its threefold mission of research, teaching and patient care. In the future, I hope to both treat patients and be at the forefront of healthcare innovation and medical advancement through the development of novel software tools to improve disease diagnosis and advance precision medicine.
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Raechel Walker
Data Science
Nominated by: CSE professors Rose Yu and Christine Alvarado
Tell us about some of your research.
As a computer science researcher in the lab of CSE and pediatrics professor Rob Knight, I characterized microbiota using convolutional neural networks, which has the possibility to help doctors make more accurate decisions about patients.
This summer I worked with Assistant Professor Rose Yu, where we created a spatiotemporal multi-resolution tensor learning model (ST-MRTL) that predicts the variation of precipitation from the mean in the Midwest. Our workshop paper was accepted into AI for Earth Sciences (co-located with NeurIPS 2020).
During fall 2020, I was a data science researcher in the lab of Professor Michael Davidson, with the School of Global Policy and Strategy and the Mechanical and Aerospace Engineering Department, where I analyzed data from the California Solar Incentive to understand the social impact and solar inequity of low-carbon transition.
As a researcher in CSE Professor Laurel Riek's Healthcare Robotics Lab, I’m designing inclusive user interfaces and control modalities for homebound students and doctors to use telepresence robots at schools and hospitals.
How has CSE helped you in this work and recognition from CRA?
My experience in the Early Research Scholars Program, as well as conducting research with professors Knight, Yu, Davidson and Riek, have been invaluable because I learned how to develop credible approaches to solving computer science research problems, and I was equipped with the knowledge to effectively communicate my research through presentations and papers. Also, I am thankful that I was given the opportunity to develop my specific research interests early on. Thank you to CSE Professor Christine Alvarado for encouraging me to become one of the undergraduate leaders of the CSE Diversity, Equity and Inclusion committee. All of the leaders in the DEI committee inspire me to promote diversity and inclusion in my career.
What are your plans after graduating?
I aspire to pursue my Ph.D. in computer science. My objective is to become a professor who conducts research at the intersection of human-computer interaction and responsible data science to redesign interactive online systems to help communities collaborate and promote transformative justice.
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Kabir Nagrecha
Computer Science
Nominated by: CSE Assistant Professor Arun Kumar
Tell us about some of your research.
I began my undergraduate research career when I was 13 years old at CSU Los Angeles. I was involved in research on applied ML projects ranging from autonomous vehicles to efficient tunnel excavation to smart building design.
My most recent contribution to the field is an efficient video inference system capable of speeding up processing time by more than five times, published as part of a paper in ACM TODS. I am also working on a model parallelism system which allows arbitrarily large models to be trained on even a single small device through a sharding process. The system can also be used to optimize training of several large models in parallel.
How has CSE helped you in this work and recognition from CRA?
In my junior year, I transferred to UC San Diego, knowing that its CSE department offered a wealth of cutting-edge research opportunities. After transferring, I began work with Assistant Professor Arun Kumar on the exciting field of ML systems, an area focused on the optimization of ML application lifecycles (data management, ML training/inference optimization, AutoML).
Throughout my research career, I’ve been able to publish five research papers (another three are under evaluation), give several conference talks, and now, receive this CRA honorable mention to recognize my work. This would not have been possible without the CSE department’s willingness to take on undergraduate researchers and its rigorous course offerings.
What are your plans after graduating?
I graduate this year and plan to pursue a Ph.D. focused on ML systems.
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McKenna Lewis
Computer Science
Nominated by: CSE professors Niema Moshiri, Christine Alvarado and Leo Porter
Tell us about some of your research.
Currently I am using mathematical models and computational approaches to study the evolution of cancer cells. Prior to this, I developed a program called SEPIA, a simulation-based Python framework for evaluating prioritization techniques used in the molecular epidemiology of viruses like HIV. During the summer I worked on CS education research, looking at student’s experiences in early computer science courses during the shift to emergency online learning.
How has CSE helped you in this work and recognition from CRA?
I have been able to collaborate with Assistant Teaching Professor Niema Moshiri (with a focus on HIV phylogenetics and epidemiology) during my participation in the Early Research Scholars Program my sophomore year, which is led by Professor Christine Alvarado. I also had the opportunity to work with Christine Alvarado this summer, along with Associate Teaching Professor Leo Porter and CSE Professor Bill Griswold (with a focus on CS education research).
The significant support I’ve gotten from these professors in the CSE department has been invaluable and exposed me to different fields of research within CSE. Their guidance and support has inspired me to keep pursuing research. Now I am working on a co-mentored project with Kit Curtius, an assistant professor of biomedical informatics at UC San Diego, and Niema Moshiri.
What are your plans after graduating?
My goals include getting a Ph.D., focusing on computational bioinformatics.