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Research helps Blugold discover how computer science, health care intersect

| Judy Berthiaume

Photo caption: Thanks to his undergraduate research, Nichol He found a way to bring his passions for computer science and health care together in his future career. After He earns his degree in software engineering, the Blugold hopes to go to medical school while also continuing his research in bioinformatics. (Photo by Jesse Yang)

Coming into college, Nichol He knew he wanted to study either computer science or pre-med, two very different academic areas that he assumed could only lead to two very different careers.

Since the University of Wisconsin-Eau Claire has strong programs in both areas, He decided he’d take a few classes in each discipline and then decide which path to follow.

“I was really interested in computer science and I knew I didn’t want to give that up,” He says, noting that while his longtime goal is to be a physician, the logic of computer science, "just really clicks with me. So, I decided to major in software engineering and minor in pre-professional health sciences. That way I could experiment with them both and decide which one I absolutely want to do.”

This summer — thanks to his work on multiple research projects — He realized he doesn’t have to choose between his two passions because computer science and health care intersect in ways he never imagined.

“All in all, it was a very powerful experience and has had a big influence on what I want to do post-graduation,” He says of his research. “Coming into the university, my hopes were to go to medical school and become a physician or to graduate and be a computer scientist. I thought I would have to give one of them up. I never thought my interests in computer science and the medical field would ever intersect.

“Now, because of my research, I’ve found bioinformatics, which really is a combination of my two passions. I really like the intersection between software engineering/computer science and the biology/medical field.”

So, his future plans now include going to medical school and specializing in radiology, and also continuing his bioinformatics research during his postgraduate studies and/or after he becomes a physician.

Embracing undergraduate research

This summer, He worked alongside two faculty research mentors, one in biology and one in computer science.

He worked with Dr. Bradley Carter, an assistant professor of biology, to study the effects of chemicals on the development of zebra fish. And he collaborated with Dr. Rahul Gomes, assistant professor of computer science, on research involving deep learning and bioinformatics.

“Both research projects are very different; they are almost complete opposites,” says He, a native of Medina, Minnesota. “One is really observing behaviors in fish and working with animals and the other is working with data and programs. They were completely different, but together they really gave me an enriching experience.”

Through his research with Gomes, He began to understand the powerful intersection between computer science and the natural sciences.

Working with researchers at North Dakota State University, He and Gomes explored methylation markers, which are certain values associated with gene expression that possibly are related and could be a predictor of pancreatic cancer.

“So, the deep learning I’m doing on this project is looking at all this data and predicting whether or not a person might have pancreatic tumors or if they are healthy,” He says.

Gomes and He also are working with Mayo Clinic Health System on a project that uses CT scans and data to help predict outcomes for patients with pancreatic cancer who are being treated with chemotherapy.

“My research over the summer was a unique experience for me because I was working in a real-world work environment,” He says. “And it showed me that I really want to explore deep learning in bioinformatics more.

“I went into this research without knowing anything about deep learning or bioinformatics. But I’ve found this passion for it and that is really, really cool.”

About bioinformatics

Bioinformatics is the science of storing, extracting, organizing, analyzing, interpreting and using biological information. It incorporates data and analytical approaches from the biological sciences, computer science, data science and mathematics.

The field of bioinformatics grew out of the need to organize and analyze the increasingly large amounts of biological data — including data critical to advances in health care — being generated. Bioinformatics analyses are increasingly necessary to address many biological questions.

“The need for bioinformatics is now greater than ever,” Gomes says. “As modern technology enables us to collect more and more clinical as well as biological data, we require experts who are not only capable of processing the data to gain information but do so in the most optimized fashion to enable a faster and more accurate response.”

A new bioinformatics major — an interdisciplinary program that draws on expertise in the university’s biology, computer science and mathematics departments — will be available at UW-Eau Claire beginning in fall 2022. It will be the only bioinformatics program of its kind in the UW System.

Exceptional student

Gomes describes He as an outstanding student and researcher, who has made valuable contributions to their research despite having no prior background in deep learning or bioinformatics.

“Nichol is very perceptive about the challenges while developing a deep learning model and how we can overcome them,” Gomes says. “During the pancreatic cancer research project with Mayo Clinic, he introduced and implemented a patch-based deep learning model to divide the CT scans in 3D patches, making model training more feasible on our GPU nodes at the Blugold Center for High-Performance Computing.

“The fact that Nichol can take in information and also engage in discussions to modify or improve the proposed workflow is simply astounding considering that he is an undergraduate student and with no prior experience in deep learning.”

A Karlgaard Scholar

He came to UW-Eau Claire primarily because of the many internship and research opportunities he knew he’d find as a Blugold.

Among the opportunities he values most is being a Karlgaard Fellow, a scholarship program that, among other things, supports undergraduate student researchers who are studying computer science or software engineering.

Karlgaard scholars collaborate with computer science faculty on research and produce scholarly publications and/or formal presentations outside of the UW-Eau Claire campus.

“I was fortunate enough to be chosen for this scholarship, and it’s been a big motivator for me to explore different areas of computer science,” He says. “Knowing there is someone who supports me financially makes me feel motivated to work harder, but it also makes me even more thankful for the opportunities.”

David and Marilyn Karlgaard met while both were students at UW-Eau Claire. David Karlgaard graduated in 1967 with degrees in math and physics. He was co-founder, CEO and president of PEC Solutions Inc., an internet technology-consulting firm, which was acquired by Nortel Networks in 2005. Marilyn Karlgaard, who attended UW-Eau Claire from 1965-1968, is a retired human resource manager.

The Karlgaards have made substantial donations to the UW-Eau Claire Foundation, gifts that support multiple scholarships and various other university initiatives.

He says the fellowship program’s ties to undergraduate research are especially meaningful because computer science majors often come into the program with a set idea of what they want to do with their degree. Research can help them discover career paths they may not have considered or otherwise known about.

“It’s a very wide field and a very fun field, so students need to look around and find the niches that fit them,” He says of computer science and software engineering. “It was being a Karlgaard Scholar that got me into this bioinformatics research. Without that, I wouldn’t even know what I want to do in the future.”