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A. Aghazadeh, A. Y. Lin, M. A. Sheikh, A. L. Chen, L. M. Atkins, C. L. Johnson, J. F. Petrosino, R. A. Drezek, R. G. Baraniuk, “Universal Microbial Diagnostics using Random DNA Probes,” Science Advances, vol. 2, 28 September 2016.

Abstract:  Early identification of pathogens is essential for limiting development of therapy-resistant pathogens and mitigating infectious disease outbreaks. Most bacterial detection schemes use target-specific probes to differentiate pathogen species, creating time and cost inefficiencies in identifying newly discovered organisms. We present a novel universal microbial diagnostics (UMD) platform to screen for microbial organisms in an infectious sample, using a small number of random DNA probes that are agnostic to the target DNA sequences. Our platform leverages the theory of sparse signal recovery (compressive sensing) to identify the composition of amicrobial sample that potentially contains novel or mutant species. We validated the UMD platform in vitro using five random probes to recover 11 pathogenic bacteria. We further demonstrated in silico that UMD can be generalized to screen for common human pathogens in different taxonomy levels. UMD’s unorthodox sensing approach opens the door to more efficient and universal molecular diagnostics.

More than 1.5 million college students have used a free textbook from OpenStax, the Rice University-publisher announced today. The number of students using OpenStax textbooks in college and high school courses has more than doubled since January 2016, and OpenStax estimates it will save students $70 million in the 2016-17 academic year.

"More than 811,000 students are using our books this fall, which is a 106% increase over spring 2016. Our books are being used in over 4,500 courses at 2,688 universities, colleges and high schools. This is 27% of all US degree-granting institutions," said Richard Baraniuk, founder and director of OpenStax and Rice's Victor E. Cameron Professor of Engineering. "Our books are making it possible for more students to afford college at a time when a college education has never been more important."

Based on the number of instructors who have notified OpenStax that they are adopting the books in their courses, OpenStax knows that 1.5 million students have used its books since 2012. Based on the date of adoptions, the one millionth student is among the students in instructor Shawna Brandle's American Government course this fall at Kingsborough Community College in Brooklyn, N.Y.

"I'm so happy to be using the OpenStax American Government textbook," said Brandle, an assistant professor of political science at Kingsborough. "I taught for years using expensive textbooks I didn't like before trying a different free digital book that wasn't great. I even tried making my own book, but nothing at any price is as good as the OpenStax book. I'm doubly happy knowing that my students are not paying for a book and are still getting the best resource available, regardless of price."

OpenStax launched in 2012 with two titles and a unique OER business model: Use philanthropic grants to produce high-quality, peer-reviewed textbooks that are free online and low-cost in print.

Current titles include College Physics; Biology; Concepts of Biology; Anatomy and Physiology; Chemistry; University Physics, volume 1; Microbiology; Sociology 2e; Principles of Economics; Principles of Macroeconomics; Principles of Microeconomics; Psychology; American Government; U.S. History; Introductory Statistics; Precalculus; Calculus, volumes 1-3; Algebra and Trigonometry; College Algebra; and Prealgebra.

College students love highlighting textbook passages while they study, and a team of researchers in three states will apply the latest techniques from machine learning and cognitive science to help turn that habit into time well-spent.

The four-year, $1 million research program at Rice University, the University of Colorado-Boulder, and the University of California-San Diego (UCSD) is one of 18 grants announced today by the National Science Foundation as part of the BRAIN Initiative, a coordinated research effort to accelerate the development of new neurotechnologies.

"Highlighting is something students naturally do on their own, and we want to create software that can use those highlights to improve both their comprehension and knowledge retention," said Phillip Grimaldi, a co-investigator on the project and research scientist at the Rice University-based nonprofit textbook publisher OpenStax.

OpenStax uses philanthropic grants to produce high-quality, peer-reviewed textbooks that are free online and used by more than 680,000 college students at more than 2,000 colleges and universities. Grimaldi said the research team plans to use OpenStax books and learning tools in a number of ways.

First, they will ask OpenStax users to volunteer their highlights for a database that can be mined for clues about the volunteers' understanding of the text. The researchers also will conduct laboratory experiments at Rice, UC-Boulder and UCSD to come up with new software that leverages the highlighted information to improve learning outcomes.

One reason the big-data approach is needed is that by itself, highlighting isn't a very effective way to learn, Grimaldi said.

"A number of studies have shown that highlighting does little to improve learning outcomes, but students tend to think that it does, and it makes them feel good about studying," he said. "At the same time, college students generally aren't willing to change how they study, so we want to piggyback on what they're already doing -- spontaneously annotating passages of text -- and turn that from a marginal activity into one that improves learning."

This project is funded by a grant from the National Science Foundation's Cyberlearning and Future Learning Technologies program. The researchers plan to create software that can predict how well students will perform on tests based on what the students highlight in their textbooks. The researchers will then create tools that use the material a student highlights to create customized quizzes and reviews for that student. The team also will try to determine the optimum time to give those quizzes and reviews to maximize comprehension and retention.

"Data from highlights supplied by OpenStax users will enable us to create tools that are both sensitive to each student's interests and robust to poor highlighting choices," said Richard Baraniuk, co-principal investigator on the project, founder and director of OpenStax and Rice's Victor E. Cameron Professor of Engineering. "The idea is to reformulate selected passages into review questions that encourage the active reconstruction and elaboration of knowledge. The design and implementation of the tool will be informed by both randomized controlled studies within the innovative OpenStax textbook platform and in coordinated laboratory studies."

CU-Boulder's Mike Mozer is the principal investigator on the grant, and co-principal investigator Hal Pashler will lead the activities at UCSD.

Read the press release

T. A. Baran, R. G. Baraniuk, A. V. Oppenheim, P. Prandoni, and M. Vetterli, “MOOC Adventures in Signal Processing: Bringing DSP to the Era of Massive Open Online Courses,” IEEE Signal Processing Magazine, Vol. 3, Issue 4, July 2016

Abstract: In higher education circles, 2012 may be known as the “year of the MOOC"; the launch of several high-profile initiatives, both for profit (Coursera, Udacity) and not for profit (edX), created an electrified feeling in the community, with massive open online courses (MOOCs) becoming the hottest new topic in academic conversation. The sudden attention was perhaps slightly forgetful of many notable attempts at distance learning that occurred before, from campus TV networks to well-organized online repositories of teaching material. The new mode of delivery, however, was ushered in by a few large-scale computer science courses, whose broad success triggered significant media attention.

Paper at IEEE Explore
Preprint at Rice DSP

M. S. Asif, A. Ayremlou, A. Sankaranarayanan, A. Veeraraghavan, and R. G. Baraniuk, "FlatCam: Thin, Bare-Sensor Cameras using Coded Aperture and Computation," arXiv preprint arxiv.org/abs/1509.00116, 2015

FlatCam is a thin form-factor lensless camera that consists of a coded mask placed on top of a bare, conventional sensor array. Unlike a traditional, lens-based camera where an image of the scene is directly recorded on the sensor pixels, each pixel in FlatCam records a linear combination of light from multiple scene elements. A computational algorithm is then used to demultiplex the recorded measurements and reconstruct an image of the scene. FlatCam is an instance of a coded aperture imaging system; however, unlike the vast majority of related work, we place the coded mask extremely close to the image sensor that can enable a thin system. We employ a separable mask to ensure that both calibration and image reconstruction are scalable in terms of memory requirements and computational complexity. We demonstrate the potential of the FlatCam design using two prototypes: one at visible wavelengths and one at infrared wavelengths.

FlatCam architecture. (a) Every light source within the camera field-of-view contributes to every pixel in the multiplexed image formed on the sensor. A computational algorithm reconstructs the image of the scene. Inset shows the mask-sensor assembly of our prototype in which a binary, coded mask is placed 0.5mm away from an off-the-shelf digital image sensor. (b) An example of sensor measurements and the image reconstructed by solving a computational inverse problem.

Press coverage:

Thanks to some recent funding from NSF, the DARPA REVEAL program, the IARPA MICrONS program, and several philanthropic foundations, we're hiring postdocs in three different areas:

Rice DSP postdoc alums have gone on to academic positions at Cornell, Columbia, CMU, Georgia Tech, U. Maryland, U. Wisconsin, U. Minnesota, NCSU, McGill, EPFL, and KU-Leuven.  Email <richb at rice dot edu> for more information.