Carnegie Mellon University
October 05, 2018

Faculty Profile: Comp Bio’s Compeau Rethinks Traditional Teaching

Phillip CompeauWhen Phillip Compeau was a child, he dreamed of being whisked away to a new kind of school, one where all the students sat at their own desks with a collection of work and a computer to guide them through it. Each student could tackle their personalized task list at their own pace. Need help? Click a button or ask the teacher. It’s no surprise, then, that Compeau — now an assistant teaching professor and Assistant Department Head for Education in Carnegie Mellon University’s Computational Biology Department — has spent much of his professional life studying not just his chosen field of computational biology, but also how students learn. And he’s worked hard to find the best strategies for teaching them.

In its simplest form, computational biology uses techniques from computer science to solve biological problems. Before computational biology was a mature discipline — CMU awarded its first undergraduate comp bio degrees in 1989, when the program lived in the Mellon College of Science — students interested in the field often majored in computer science and took bio courses, or maybe studied bio with some work in computer science. In Compeau’s case, it was math.

As an undergrad at Davidson College in his home state of North Carolina, Compeau studied math but worked at its intersection with biology. Specifically, his senior thesis focused on a variant of the pancake-sorting problem: determining the minimum number of spatula flips necessary to transform a stack of differently sized pancakes into a pyramid shape. “If you think of the pancakes as different genes, and the flips as certain large-scale mutations, then pancake-sorting offers a model for transforming one chromosome into another,” Compeau said. He also played competitive tennis and at one point had an Association of Tennis Professionals (ATP) ranking in doubles. But that’s beside the point.

After a brief excursion to Cambridge University, where he earned a master of advanced study degree in mathematics, Compeau headed west to work with noted computational biologist Pavel Pevzner at the University of California, San Diego. While there, his focus changed.

“I did research during my Ph.D. years, but the larger effort I undertook was doing online educational projects and building an online textbook,” Compeau said. “I decided I wanted to be a teaching-track professor, which is not the most common ambition. I was fortunate enough to be in an environment with an advisor who could support that.”

While at UCSD, Compeau co-founded Rosalind, an online platform for learning bioinformatics through problem-solving. He also co-instructed the first massive open online course (MOOC) in bioinformatics. Both initiatives have since exploded. Rosalind has reached more than 50,000 people and has been adopted more than 100 times by universities for offline courses. The MOOC has evolved into the bioinformatics specialization on Coursera and its best-selling print companion, “Bioinformatics Algorithms: An Active Learning Approach.” The course has been completed by a few thousand learners and used in some way by more than 200,000 people.With Rosalind and the MOOC under his belt, Compeau joined the Computational Biology Department faculty in 2015.

“What brought me to CMU was the fact that it has a good history of prioritizing teaching-track faculty and seeing the value in them,” he said. “It’s a rare environment to have an entire department devoted to computational biology, as well as to be a university that prioritizes teaching.”

Since arriving in Pittsburgh, Compeau has made substantial contributions to the department. In his role as assistant department head for education, he led the creation of the undergraduate degree in computational biology, which he directs and whose students he advises. It’s the only comp bio degree granted from a school of computer science.

“Because SCS is so strong at the undergrad level, we can design a major that simply wouldn’t be possible at other places,” Compeau said. “Students hit the ground running in math and science here, and it means that we can teach them computational biology at a deep level. And that means we can produce graduates who fill a huge area of need for solving the big biological and medical problems of the 21st century.”

Compeau also collaborated with fellow comp bio teaching professor Josh Kangas to develop the first precollege computational biology program in the U.S. The program, slated to begin this summer, will first put students in the lab and then in front of computers to analyze the data they generate. “It’s going to be an amazing experience for them,” Compeau said.

Like his young self, grown-up Compeau still believes there’s massive room for using automation to improve education. In his own courses, he’s implemented a flipped classroom and relies on active learning. No traditional lectures here. Students complete reading assignments in an interactive textbook before the class meeting, and spend in-class time working on challenge problems and answering questions from their peers to cement their learning.

His strategy, while successful, requires a complete rethinking of learning. And it requires student buy-in.

"We indoctrinate students into thinking they can only learn one way,” Compeau said. “Teachers are considered the fountain of knowledge, and when that source of wisdom is asking students to solve problems and guiding them to figure out solutions on their own instead. … Well, some people have an allergic reaction to that.”

To tame that allergy, Compeau spends the first day of his course selling the format to his students by outlining the weaknesses of traditional lectures, the goals of the course and how the flipped course will benefit them. So far, he’s seen positive course evaluations and a significant improvement in test scores.

While he’s made great strides toward building a student-centric classroom, Compeau still hasn’t created that fantasy school of his first-grade dreams. But he doesn’t want to. “Removing the teacher from the picture entirely is a naïve view,” he said. “The modern classroom should find ways to use online materials to improve our teaching — not to replace it.” And at Carnegie Mellon, he’s happy to have found a cohort of colleagues willing to do whatever it takes to give students the best education possible.

He still, occasionally, plays tennis. These days, though, he’s more of a golfer.