Undergraduate Students Win International Data Science Competition


Undergraduate students Hongsen Qin, Emma Qian, Thomas Hoffmann, and Alexander Zlokapa (advised by Professors Aaron Ames, Erik Winfree, Jonathan Katz, Maria Spiropulu, and Yaser Abu-Mostafa) have won the Citadel Data Open International Data Science Competition. This winning team chose to investigate the optimal way to spend $1 billion to save lives from malaria and sanitation-related diseases, allocating funds for different prevention methods and optimizing budget breakdowns country by country. To quantify the socioeconomic impacts of their policy proposal, they modeled a variety of aspects from mosquito feeding cycles to climate change using techniques ranging from causal discovery methods to interpretable machine learning. The Caltech team was among 24 teams that were evaluated and questioned by a panel of experts including the former Chief Scientist of AI at Microsoft, a Princeton professor, and the chief of equities at Citadel. The Caltech team was chosen as the first place winner based on the depth, rigor, and comprehensiveness of their analysis.

Tags: EE honors CMS Erik Winfree Yaser Abu-Mostafa Aaron Ames Hongsen Qin Emma Qian Thomas Hoffmann Alexander Zlokapa

Computer Scientists Create Reprogrammable Molecular Computing System


Erik Winfree, Professor of Computer Science, Computation and Neural Systems, and Bioengineering, and colleagues have designed DNA molecules that can carry out reprogrammable computations, for the first time creating so-called algorithmic self-assembly in which the same "hardware" can be configured to run different "software." Although DNA computers have the potential to perform more complex computations than the ones featured in the Nature paper, Professor Winfree cautions that one should not expect them to start replacing the standard silicon microchip computers. That is not the point of this research. "These are rudimentary computations, but they have the power to teach us more about how simple molecular processes like self-assembly can encode information and carry out algorithms. Biology is proof that chemistry is inherently information-based and can store information that can direct algorithmic behavior at the molecular level," he says. [Caltech story]

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Professor Winfree Elected to American Association for the Advancement of Science


Erik Winfree, Professor of Computer Science, Computation and Neural Systems, and Bioengineering, has been elected as a Fellow of the American Association for the Advancement of Science (AAAS) which is the world's largest general scientific society. Professor Winfree was recognized for his "foundational contributions to biomolecular computing and molecular programming." [Caltech story] [ENGenious feature]

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2015 Bhansali Prize Award Winners


Bryan He, a senior student advised by Yisong Yue, and William Hoza, a junior student advised by Leonard Schulman, are the recipients of the 2015 Bhansali Prize. Nicholas Schiefer, a junior student advised by Erik Winfree, won an honorable mention for the Prize. The Bhansali Prize is typically awarded to one undergraduate student for outstanding research in Computer Science in the current academic year, but due to the number of particularly high-caliber candidates in 2015, the Bhansali Prize committee determined that multiple students deserved the award.

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Best Paper in Distributed Computing


The paper, “Speed faults in computation by chemical reaction networks,” written by graduate student Rachel A. Cummings who is advised by Professor Katrina Ligett, Senior Research Fellow David Doty working in Professor Erik Winfree’s lab, and colleagues has received the best paper award at this year’s International Symposium on Distributed Computing. [Read the paper]

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Building Artificial Cells Will Be a Noisy Business


Erik Winfree, Professor of Computer Science, Computation and Neural Systems, and Bioengineering, explains, "I tend to think of cells as really small robots. Biology has programmed natural cells, but now engineers are starting to think about how we can program artificial cells. When I program my computer, I can think entirely in terms of deterministic processes. But when I try to engineer what is essentially a program at the molecular scale, I have to think in terms of probabilities and stochastic (random) processes. This is inherently more difficult, but I like challenges. And if we are ever to succeed in creating artificial cells, these are the sorts of problems we need to address." [Caltech Release]

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Molecular Programming Research Wins A Second $10 Million Award


Professor Erik Winfree and colleagues have won a second $10 million award for research in molecular programming. "Computer science gave us this idea that many tasks can actually be done with different types of devices," Winfree says. For example, a 19th-century cash register and a 21st-century computer can both be used to calculate sums, though they perform the same task very differently. At first glance, writing a computer program and programming a DNA molecule may seem like very different endeavors, but "each one provides a systematic way of implementing automated behaviors, and they are both based on similar principles of information technology," Winfree says. This Expeditions in Computing Award will be used to take their work in molecular programming to the next level: from proof-of-principle demonstrations to putting the technology in the hands of users in biology, chemistry, physics, and materials science. [Caltech Release]

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Robust Self-Replication


Erik Winfree, Professor of Computer Science, Computation and Neural Systems, and Bioengineering, and colleagues including Caltech alumnae Rebecca Schulman, have created a new system to copy sequence information. In their approach, tiny DNA tile crystals consisting of many copies of a piece of information are first grown, then broken into a few pieces by mechanically-induced scission, or force. The new crystal bits contain all the information needed to keep copying the sequence. Each piece then begins to replicate its information and grow until broken apart again—without the help of enzymes, an essential ingredient in biological sequence replication. [Caltech Press Release]

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DNA Robotics Research Earns Undergrads a Gold Prize


Undergraduate students Zibo Chen, Shayan Doroudi, Yae Lim Lee, Gregory Izatt, and Sarah Wittman have won a gold award at the 2011 International Bio-Molecular Design Competition (BIOMOD). BIOMOD is a competition for undergraduate teams who design research to address the control of biomolecules on the nanometer scale. The Caltech team's challenge was to make a synthetic DNA robot that has the ability to take a random walk —instead of walking on set path or track—on a two-dimensional origami surface that was also made out of DNA. The team is mentored by Professor Erik Winfree and sponsored by the Molecular Programming Project. [Caltech Feature] [Video of Project]

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First Artificial Neural Network Created Out of DNA


Lulu Qian, Senior Postdoctoral Scholar in Bioengineering; Erik Winfree, Professor of Computer Science, Computation and Neural Systems, and Bioengineering; and Jehoshua (Shuki) Bruck, Gordon and Betty Moore Professor of Computation and Neural Systems and Electrical Engineering, are the first to have made an artificial neural network out of DNA, creating a circuit of interacting molecules that can recall memories based on incomplete patterns, just as a brain can. [Caltech Press Release]

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