Nina Amenta: Looking for patterns and collaborations in the data

by Gordy Slack

Professor Nina Amenta is the new director of CITRIS@Davis.

Nina Amenta has done her share of deep mathematics and computational analysis. She continues to make discoveries in those rarified realms developing, for example, the best ways to exploit the parallel computing potential of graphic processing units that now come along with most personal computers. But at 53, the UC Davis professor of computer science says she is compelled to get involved in research that will “have real world impact in other areas.”

In that way, she is the ideal person to lead CITRIS at UC Davis, a job she assumed late last year.

Amenta has a growing sense of urgency about the need to address climate change. “We could be looking at terrible consequences in terms of agriculture, sea-level rise, and increasingly intense weather patterns,” she says. “I don’t understand why people are not taking it much more seriously.”

Part of the challenge is communication, both between different departments and more broadly with the general public, she says. “At some level people know that there’s a problem, but they look out the window and see that it’s a beautiful day and they say, ‘What environmental problem? What climate change?’”

There are plenty of people at UC Davis taking the threat of rapid and radical climate change very seriously, though.  For example, researchers in the Center for Watershed Sciences are working to understand and reform the way water moves through California, and how that may change in coming decades. At the Energy Efficiency Center, researchers look for strategies for reducing energy use in buildings, transportation, and agriculture.  And in her new role as the campus director of CITRIS, Amenta will help IT researchers collaborate more effectively with people like this at Davis who are working on climate related issues.

Amenta also wants to get more Davis IT researchers involved with CITRIS activities at the UC Davis Medical Center, led by Chief Scientist Dr. Tom Nesbitt. “Tom has this great vision of telemedicine improving care and at the same time reducing costs,” she says. “Monitoring a diabetes patient using their phone, or letting a patient visit a specialist through video conferencing, rather than driving for two hours, just makes so much sense in today’s environment.” 

Amenta’s work in computer visualization also intersects with her real-world concerns, and with CITRIS’s unusual approach to interdisciplinary collaborations. Amenta welcomes the opportunity CITRIS presents for people in computer science and electrical engineering to work with artists and people in the humanities who are adept at “bringing data to people in a way that makes it useful,” she says.

Back in Pittsburgh in the 1970s, while still in high school, Amenta’s love of math and computation was in fact mostly aesthetic. She loved the artwork of M.C. Escher, the Dutch artist known for mathematically-inspired prints that employ repeating patterns.  Amenta enjoyed figuring out her own schemes and carefully drawing them. “I loved seeing patterns,” she says. “This was long before the web, so I went to the library at Carnegie Mellon University and looked through their math books trying to figure out what kinds of repeating patterns I could make and what the mathematical rules were that governed them,” she says.

That affection for patterns reappeared in a summer graduate school project at UC Berkeley in the 1990’s,  where she wrote a program that would replicate a pattern and tessellate it in one of the 17 possible ways to completely cover the plane. Her original project, called Kali, was written for a long-extinct SGI machine but has since been modified and developed by topologist Jeff Weeks;  Mac and Window versions of Kali can still be found online.

Amenta’s main research field is computational geometry, a branch of computer science that develops algorithms for geometric problems, like those that arise in computer graphics.  This is a line of work in keeping with her original geometric fascinations. She is currently working on an effort to more fully exploit the parallel processors found in Graphic Processing Units (GPUs), the chips mostly dedicated to processing graphics, now found in virtually all personal computers, for geometric problems. 

“For as long as I have been in computer science, people have been saying, “In the future everything is going to be massively parallel,” Amenta says. “But that future has been slow in coming: it is hard to design massively parallel machines and it is very difficult to program them. And the algorithms you use on parallel machines are often very different than the ones that you use on a regular sequential computer. So even though these chips are common, they are still very hard to program. But getting students to work on this stuff is a piece of cake. To them it is like driving a racecar.”

Amenta collaborated with C.U.N.Y. anthropologist Eric Delson on a project modeling the continuous change in primate skull morphology on an evolutionary timescale.

Some of Amenta’s early and most influential work involved creating smooth-surfaced 3D models from clouds of measured points, often taken by a laser scanner, from real-world objects. One of her other current research grants is a collaboration with C.U.N.Y. physical anthropologist Eric Delson.  It is an effort to model the gradual evolutionary change of primate species over time by combining laser scanner models of the skulls of existing and fossil species, with an evolutionary tree computed based on genomic data like DNA. By creating an “evolutionary morph,” Amenta has allowed anthropologists to watch how skulls from several different species, but with a single common ancestor, changed over evolutionary time as they grew more distant from the common ancestor and each other.  Amenta is also collaborating with Corey Toler-Franklin, a Yale Postdoctoral Fellow in computer science visiting at UC Davis. Toler-Franklin is investigating new, scientifically accurate methods of capturing and analyzing these biological specimens.

By quantifying these morphological differences between complex specimens evolutionary biologists would have a useful tool for gauging evolutionary relationships between skeletal specimens for which there may be no DNA to analyze.  Finding better ways to do this is one of the goals in Amenta’s current project.

These are still early days for Amenta at CITRIS@Davis, but she already relishes her new role bringing people from different parts of UC Davis, and from different campuses, together to form novel partnerships. “I have a history of talking to people in completely different fields and putting together productive collaborations. I like to figure out where the right collaborators are and how, with the help of IT, they can make a bigger impact.”