Nav: Home

From viruses to social bots, researchers unearth the structure of attacked networks

May 29, 2019

The human body's mechanisms are marvelous, yet they haven't given up all their secrets. In order to truly conquer human disease, it is crucial to understand what happens at the most elementary level.

Essential functions of the cell are carried out by protein molecules, which interact with each other in varying complexity. When a virus enters the body, it disrupts their interactions and manipulates them for its own replication. This is the foundation of genetic diseases, and it is of great interest to understand how viruses operate.

Adversaries like viruses inspired Paul Bogdan, associate professor in the Ming Hsieh Department of Electrical and Computer Engineering, and recent Ph.D. graduate, Yuankun Xue, from USC's Cyber Physical Systems Group, to determine how exactly they interact with proteins in the human body. "We tried to reproduce this problem using a mathematical model," said Bogdan. Their groundbreaking statistical machine learning research on "Reconstructing missing complex networks against adversarial interventions," was published in Nature Communications journal earlier this April.

Xue, who earned his Ph.D. in electrical and computer engineering last year with the 2018 Best Dissertation Award, said: "Understanding the invisible networks of critical proteins and genes is challenging, and extremely important to design new medicines or gene therapies against viruses and even diseases like cancer."

The 'protein interaction network' models each protein as a 'node.' If two proteins interact, there is an 'edge' connecting them. Xue explained, "An attack by a virus is analogous to removing certain nodes and links in this network." Consequently, the original network is no longer observable.

"Some networks are highly dynamic. The speed at which they change may be extremely fast or slow," Bogdan said. "We may not have sensors to get accurate measurements. Part of the network cannot be observed and hence becomes invisible."

To trace the effect of a viral attack, Bogdan and Xue needed to reconstruct the original network by finding a reliable estimate of the invisible part, which was no easy task. Said Bogdan: "The challenge is that you don't see the links, you don't see the nodes, and you don't know the behavior of the virus." To solve this problem, Xue added, "The trick is to rely on a statistical machine learning framework to trace all possibilities and find the most probable estimate."

In sharp contrast to prior research, the lab's novel contribution is that they actively incorporate the influence and causality of the attack, or 'adversarial intervention', into their learning algorithm rather than treat it as a random sampling process. Bogdan explained, "Its real power lies in its generality - it can work with any type of attack and network model."

Due to the generality of their proposed framework, their research has far-reaching applications to any network reconstruction problem involving adversarial attack, in diverse fields such as ecology, social science, neuroscience, and network security. Their paper has also demonstrated its capability to determine the influence of trolls and bots on social media users.

Bogdan plans to extend their work by experimenting with a range of attack models, more complex and varied datasets, and larger network sizes to understand their effect on the reconstructed network.
-end-


University of Southern California

Related Proteins Articles:

New method to monitor Alzheimer's proteins
IBS-CINAP research team has reported a new method to identify the aggregation state of amyloid beta (Aβ) proteins in solution.
Composing new proteins with artificial intelligence
Scientists have long studied how to improve proteins or design new ones.
Hero proteins are here to save other proteins
Researchers at the University of Tokyo have discovered a new group of proteins, remarkable for their unusual shape and abilities to protect against protein clumps associated with neurodegenerative diseases in lab experiments.
Designer proteins
David Baker, Professor of Biochemistry at the University of Washington to speak at the AAAS 2020 session, 'Synthetic Biology: Digital Design of Living Systems.' Prof.
Gone fishin' -- for proteins
Casting lines into human cells to snag proteins, a team of Montreal researchers has solved a 20-year-old mystery of cell biology.
Coupled proteins
Researchers from Heidelberg University and Sendai University in Japan used new biotechnological methods to study how human cells react to and further process external signals.
Understanding the power of honey through its proteins
Honey is a culinary staple that can be found in kitchens around the world.
How proteins become embedded in a cell membrane
Many proteins with important biological functions are embedded in a biomembrane in the cells of humans and other living organisms.
Finding the proteins that unpack DNA
A new method allows researchers to systematically identify specialized proteins called 'nuclesome displacing factors' that unpack DNA inside the nucleus of a cell, making the usually dense DNA more accessible for gene expression and other functions.
A brewer's tale of proteins and beer
The transformation of barley grains into beer is an old story, typically starring water, yeast and hops.
More Proteins News and Proteins Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Listen Again: Reinvention
Change is hard, but it's also an opportunity to discover and reimagine what you thought you knew. From our economy, to music, to even ourselves–this hour TED speakers explore the power of reinvention. Guests include OK Go lead singer Damian Kulash Jr., former college gymnastics coach Valorie Kondos Field, Stockton Mayor Michael Tubbs, and entrepreneur Nick Hanauer.
Now Playing: Science for the People

#562 Superbug to Bedside
By now we're all good and scared about antibiotic resistance, one of the many things coming to get us all. But there's good news, sort of. News antibiotics are coming out! How do they get tested? What does that kind of a trial look like and how does it happen? Host Bethany Brookeshire talks with Matt McCarthy, author of "Superbugs: The Race to Stop an Epidemic", about the ins and outs of testing a new antibiotic in the hospital.
Now Playing: Radiolab

Dispatch 6: Strange Times
Covid has disrupted the most basic routines of our days and nights. But in the middle of a conversation about how to fight the virus, we find a place impervious to the stalled plans and frenetic demands of the outside world. It's a very different kind of front line, where urgent work means moving slow, and time is marked out in tiny pre-planned steps. Then, on a walk through the woods, we consider how the tempo of our lives affects our minds and discover how the beats of biology shape our bodies. This episode was produced with help from Molly Webster and Tracie Hunte. Support Radiolab today at Radiolab.org/donate.