CS 101: Grading

Applications of Computer Science

Why study computer science? In fact, computer technology is often central to much scientific research. This research requires not just domain experts, such as medical and environmental researchers, but also people with deep knowledge of computer technology who are able to develop algorithms and complex applications to facilitate scientific research.

Over the course of this semester, I will add news articles to this page highlighting the many roles computers play in these scientific advancements and the many opportunities that are available for those interesting in applying their computer science expertise in ways that are deeply meaningful to humanity.

Health and Medicine

Virtual Surgery Becoming a Reality - CNN, October 17, 2007: Virtual reality's growing role in medicine was demonstrated in early October when two doctors in Argentina successfully completed their first laparoscopic gastric sleeve surgery while being monitored by their mentor in Baltimore, Md.. The communication was made possible by the Remote Presence Robot (RP-7), which makes possible high-quality, real-time audio and video communication. The mentoring surgeon, Dr. Alex Gandsas, secured a grant from RP-7's manufacturer so a RP-7 could be sent to Argentina. Two more remote observation surgeries are expected to take place sometime in November. In another case, virtual reality software was used to perform life-saving surgery on a brain aneurysm. "We have a software program available with one of our rapid CAT scanners which allows us to generate 3D images and then rotate them in ways that is relevant to rehearsing for a surgical approach," says Dr. Vini Khurana, who performed the procedure. The 3D image was projected onto one side of Khurana's eyepiece during the procedure. Other technologies still in development include mixed reality operating theatres and a medical specialty called interventional radiology that involves pinhole surgery using needles and catheters that are guided by touch and imaging.
MIT Model Could Improve Some Drugs' Effectiveness - MIT News, September 23, 2007: A computer modeling approach developed at MIT could improve a class of drugs based on antibodies by predicting which structural changes in an antibody will improve its effectiveness. The model examines a specific antibody and runs through possible amino-acid substitutions, calculating which substitutions would create a more effective interaction with the target. The model was created using both laboratory experiments and computer simulations by MIT professors Dane Wittrup and Bruce Tidor. "Making drugs out of huge, complicated molecules like antibodies is incredibly hard," says Janna Wehrle, who supervises computational biology grants at the National Institute of General Medical Sciences, which backed the research. "Dr. Tidor's new computational method can predict which changes in an antibody will make it work better, allowing chemists to focus their efforts on the most promising candidates. This is a perfect example of how modern computing can be harnessed to speed up the development of new drugs." The MIT model has already been used to create a new version of cetuximab, a drug commonly used to treat colorectal cancer, that is 10 times more effective at binding to the target than the original drug.
Computers help chemists in superbug battle - vnunet.com, August 21, 2007: Researchers in Canada say computer analysis of drugs can be used to quickly come up with emergency medications if new infectious agents and antibiotic-resistant superbugs appear. "In the case of new infectious threats, there might be no time to develop a completely new drug 'from the ground up' as the corresponding toxicological studies and regulatory investigations will take years to complete properly," says Artem Cherkasov, of the University of British Columbia in Vancouver. The scientists plan to use a new computer system to identify vulnerable cellular components of a pathogen using proteomics. Cherkasov says they will enter the key structures into the system, and use some aspects of artificial intelligence to determine which drugs have the best chance for activity against the target and for antimicrobial activity. The highest-rated compounds then could be tested in a laboratory against the pathogen and eventually used to treat people who have become infected. New developments in chemo-informatics, which combines chemistry and computer science, have made it possible to use computational models to search for "antibiotic likeness."
Semantic Web helps protect public health - ComputerWorld, July 27, 2007: Better safeguards against public health threats are being provided through new, Semantic Web-based methods for fast analysis of complex data sets from multiple sources and systems whose schema are disparate and often non-interoperable. This is the approach of a team led by Parsa Mirhaji, director of the Center for Biosecurity and Public Health Information Research at the University of Texas in Houston. Mirhaji's team developed a complex analysis engine called Sapphire (Situational Awareness and Preparedness for Public Health Incidents using Reasoning Engines) through the employment of Semantic Web technology. Sapphire's first trial took place two summers ago when massive numbers of Hurricane Katrina refugees--many of whom were in poor health--were housed in Houston, raising the risk of disease outbreaks. Sapphire was able to identify several infections in time for health officials to curtail their proliferation beyond small initial populations.
Breakthrough Approach Matches Tumor Profiles to Best Possible Anticancer Treatments - UVA Today, July 24, 2007: University of Virginia researchers Dan Theodorescu, an oncologist and cancer biologist, and Jae Lee, a computational biologist and bioinformatics statistician, have developed an algorithm that could help rapidly sort through molecular information on a patient's tumor to help find the right drug treatment as quickly as possible.
Computerized Matching System Could Enable National Kidney Exchange - June 11, 2007: Of the 70,000 some Americans awaiting kidney transplants, about 4,000 will die each year. Currently in the United States, kidney exchanges are considered the best way to increase the number of kidney transplants. Computer scientists at Carnegie Mellon University have developed a new method that can match living kidney donors with kidney disease patients, and increase the number of kidney transplants. Matches between kidney donors and recipients are determined by a specific algorithm that can search through the large national pools of donors and recipients.

Environment

Supercomputer Makes Near-Instant Movies of California Quakes - LiveScience.com, July 30, 2007: Supercomputers at the San Diego Supercomputer Center (SDSC) are being used to produce animated movies of earthquakes with magnitudes of 3.5 or greater striking Southern California. SDSC will analyze data collected from hundreds of sensors measuring ground motion in the region and create a computer model for rendering a simulation of an earthquake.

Privacy

A Little Privacy, Please - Scientific American, July 2007: Director of Carnegie Mellon University's Laboratory for International Data Privacy Latanya Sweeney is dedicated to upholding people's privacy in an increasingly security-conscious world through the development of software. According to Sweeney, the ultimate solution is the upfront incorporation of privacy protection into the design and usability of new technologies by engineers and computer scientists. "Society can [then] decide how to turn those controls on and off," she reasons.

Sociology

Bet on It! - IEEE Spectrum, September 2007: Software and services that help companies tap the "wisdom of crowds" to project public response to new products, sales revenue, or the price of new commodities are being developed and marketed. These services essentially establish a stock market of ideas, and France-based financial consultant Chris F. Masse forecasts that one out of 10 Fortune 500 companies will have publicly disclosed their use of internal prediction markets while another 10 percent will be experimenting with some projects by the end of the decade. The adoption of prediction markets in the United States is such that a group of notable economists released a statement requesting that such markets be exempted from gambling regulations, noting that "using these markets as forecasting tools could substantially improve decision making in the private and public sectors."
The Scientific Research Potential of Virtual Worlds - Science, July 27, 2007: Online virtual worlds, like Second Life and World of Warcraft, can be useful research tools for behavioral, social, and economic science, along with human-oriented computer science, writes William Sims Bainbridge of the National Science Foundation's Division of Information and Intelligent Systems.

Biology

Computers Show How Bats Classify Plants According to Their Echoes - ScienceDaily, March 24 2008: A team of machine learning scientists and experts on bats have developed an algorithm that is capable of demonstrating how bats use echoes to classify food sources. Bats emit ultrasonic pulses and are able to determine different plants according to the various echoes they pick up in return. Matthias Franz from the Max Planck Institute of Biological Cybernetics, and Yossi Yovel, Peter Stilz, and Hans Ulrich-Schnitzler from the University of Tubingen in Germany were among the researchers who used a sonar system to emit bat-like, frequency-modulated ultrasonic pulses, and then recorded thousands of echoes from live plants. Their algorithm used the time-frequency information of these echoes to classify plants. The algorithm was very accurate, and suggested why bats may be able to understand certain echoes better than others.
Social Networking for Zebra - Science News, December 1, 2007: There is considerable variation in social structures between different species, and theoretical tools that are being developed to help understand this variation could also help track terrorists, recommend products to consumers, and control disease epidemics. Princeton University ecologist Dan Rubenstein graphed the social interactions of Grevy's zebras and onagers, and found substantial differences between the two species through his application of network theory. But a key problem for Rubenstein was figuring a way to analyze changing networks, so he turned to University of Illinois in Chicago computer scientist Tanya Berger-Wolf, who took on the challenge of devising the necessary computational methods with the help of a $900,000 National Science Foundation grant. The first step of the project involved reworking the most fundamental network theory concepts so that they can operate in a graph that shows changes over time, and Berger-Wolf detailed her new techniques at the International Conference on Knowledge Discovery and Data Mining. She says that as she and others create new computational techniques, their research will enable biologists to make completely novel inquiries. "This is a beautiful example of computer science, because there are some questions biologists cannot even ask before we do the computational analysis," Berger-Wolf notes.
A Computer Simulation Shows How Evolution May Have Speeded Up - Weizmann Institute of Science, August 28, 2007: Researchers at the Weizmann Institute of Science's Molecular Cell Biology and Physics of Complex Systems Departments have developed computer simulations that mimic natural evolution, allowing the researchers to observe and manipulate the evolutionary process. Nadav Kashtan, Elad Noor, and Uri Alon simulated a population of genomes evolving over time toward a given goal. The researchers found in the simulation that changing environmental conditions sped up the evolution of the genome. More complex and complicated goals, which would take more generations to reach under fixed conditions, also accelerated the evolution process to reach changes in the goal.
3D models provide virtual approach to plant optimisation - EUREKA, August 7, 2007: Currently, farmers and commercial nurseries are required to grow crops in real time to experiment and find the optimal growing conditions through the manipulation of irrigation, spraying temperature, and nutrients, but a new computer model that combines computer science, biochemistry, and horticulture provides a much faster model of plant behavior and growing conditions. The computer model will allow farmers to make better use of resources, produce better and less expensive food, and learn more effective crop management.
The Bytes and the Bees - PC Magazine, July 11, 2007: Technology is enabling researchers to learn more about nature, with hopes of applying such insights to human problems. With biomimetics, researchers hope to develop computer technology that will be able to learn, adapt to change, and protect and repair itself. Biomimetics' influence already can be seen in developments such as IBM's Airgap Microprocessor, which was inspired by the self-assembly methods of snowflakes. An algorithm that optimizes Internet servers is based on honeybee colonies, and Melanie Mitchell, a computer science professor at Portland State University, is using the theory of natural selection to determine the best search parameters for multimedia searches.

Astronomy

Software Coordinates 19 Mirrors, Focuses James Webb Space Telescope - NASA News, August 24, 2007: NASA researchers have successfully tested a series of algorithms and software programs, known as the "Wavefront Sensing and Controls," that will control 19 mirrors in the James Webb Space Telescope so all the mirrors act as a single, highly sensitive telescope. The telescope works by taking a digital picture of a star. The image is then processed through mathematical algorithms to calculate the mirror adjustments needed to focus the image. NASA says that when properly aligned, the mirrors will allow the Webb Telescope to capture dim light from objects at the edges of space and time with extraordinarily sharp clarity.

Human Assistance

The Google Earth Outreach program combines Google Earth, Google Maps, and the United Nations High Commissioner for Refugees (UNHCR) office in an effort to highlight refugee work done by various humanitarian agencies. Participating groups can upload text, audio, and video information to Google Earth to highlight challenges faced by workers on the ground and how they intend to solve them. The new Google Earth program is divided into three layers. The first layer highlights three major areas where displaced persons are housed. The second layer explores issues such as refugee health, education, water, and sanitation through pop-up windows that explain the specific needs of each location. The third level explains issues at the local level, such as problems with schools and other infrastructure needs. UNHCR says the project will eventually allow the agency to build a geographic record of ground efforts to aid refugees that could be used for future logistical planning. Last year, Google partnered with the U.S. Holocaust Museum to launch the Genocide Prevention Mapping Initiative, an online site to help educate Web users about genocide. The site includes photographs, data, and eyewitness testimony from numerous sources about the crisis in Sudan's Darfur region.
Software Strikes a Chord for Disabled Students - eSchool News, November 29, 2007: Rensselaer Polytechnic Institute's "Adaptive Use Musical Instruments for the Physically Challenged" program enables students with severe physical disabilities to make music by just moving their heads. The system uses a digital video camera to track a student's head movements on a computer screen and then translates the movements into piano scales or drum beats. Zane Van Dusen, a RPI undergraduate student in computer science and electronic media arts and communication, developed the idea of using a digital video camera to track the user's head. A cursor is digitally placed on a portion of the student's head, usually the tip of the nose, to follow the user's movements. As the cursor moves, sounds are created based on the user's movements. Moving the head completely in one direction will create a scale climb on the piano or a quick series of drum beats or a drum roll. The project's ultimate goal is to eventually enable students to compose their own pieces to help students learn the creative process and build communication skills. "The client or patient doesn't have to be a musician to participate," says the American Musical Therapy Association's Al Bumanis. "The goal is not usually a performance, it's increasing communication skills, understanding, relearning lost skills."
New Technology Can be Operated by Thought, Science Daily, November 9, 2007: Physically disabled people can compose and send emails and operate a television by thought thanks to advances in brain-machine interface (BMI) technology, and further breakthroughs may even make the mental operation of prosthetic limbs a reality in time. Thought-controlled operation of PCs by severely handicapped patients has been facilitated by a brain computer interface (BCI) developed by the Wadsworth Center in Albany, N.Y., and Wadsworth Center researcher Eric Sellers says the system can conceivably function with little technical oversight and offer significant improvements to communication and quality of life. Meanwhile, Washington University School of Medicine researchers have developed a BCI that allows individuals to mentally control a cursor on a computer screen, a wheelchair, and a robotic arm, and a current focus is the use of the BCI to improve the rehabilitation of stroke and brain injury patients using data demonstrating that one hemisphere of the brain can compensate for functions impaired by damage to the other hemisphere.
Technique Links Words to Signing - BBC News, Sept. 15, 2007: IBM researchers have developed SiSi, a system that translates spoken words into British Sign Language (BSL). SiSi, short for say it sign it, enables deaf people to have simultaneous sign language interpretations whenever a human interpreter is not available, and could possibly be used for signing for television, radio, and telephone calls. SiSi uses speech recognition to animate a digital character. SiSi has already been approved by the Royal National Institute for Deaf people (RNID). SiSi was developed by students during a 12-week initiative called Extreme Blue that IBM hosts.
Internet Volunteers Transform Search and Rescue - New Scientist, September 29, 2007: Volunteers sifted through satellite photos on the Internet to search for the missing plane of millionaire aviator Steve Fossett, and in the process discovered the wrecks of eight other downed aircraft, illustrating the potential of "crowd-sourced" search. "The Internet is probably the only way you can do a massive search cost-effectively," says FireBall Information Technologies President Tim Ball. The search for the missing millionaire is only the second time crowd-sourcing has been tapped as a search tool. In the first instance, which was instigated by the disappearance of Microsoft research engineer Jim Gray, organizers coaxed satellite operators GeoEye and Digital Globe to contribute satellite images of the search area with 1-meter resolution, which were then segmented and sent to online volunteers using Amazon's Mechanical Turk Web site for examination. Each image sent to examiners searching for Fossett covered an 85-square meter area and was sent to 10 online volunteers; images flagged by the majority of the volunteers were prioritized for viewing by the U.S. Civil Air Patrol or Air National Guard teams. These search and rescue missions are unique in that the people being searched for were well connected, which begs the question whether similar efforts would be made for less well-connected people. The chief difficulty of mounting such missions is companies' reluctance to donate satellite imagery, and there is no assurance that the satellites will pass over a given area precisely when they are needed. Meanwhile, a 160-megapixel camera and image-processing system developed by FireBall and San Francisco's High Altitude Mapping Mission that can reportedly image "state and nation-sized areas" from an altitude of 20,000 feet is currently being test flown.

Music

Microsoft Creates 'Instant Backing Band' for Singers - New Scientist, April 7, 2008: Microsoft Research has developed MySong, software that takes a sung vocal and generates a file containing the sequence of sung notes, a process known as "pitch tracking," and uses that sequence to create backup music using a technique called "chord probability computation." The software was developed by Microsoft Research's Dan Morris and Sumit Basu and the University of Washington's Ian Simon. "The idea is to let a creative but musically untrained individual get a taste of song writing and music creation," Morris says. "There was nothing out there that could take a sung vocal melody as an input and then generate appropriate chords to accompany it." MySong compares the sung melody to the 12 standard musical notes and then feeds an approximate sequence of notes to the system's chord probability computation algorithm, which uses an analysis of 300 songs to recognize fragments of melody and chords that complement each other. To choose the best accompaniment, the user slides an on-screen bar to set the musical tone, choosing between options such as "happy factor" and "jazz factor." MIT researcher and composer Tod Machover says he is impressed with the system and notes that voice remains under-exploited in interactive systems. Machover says the software will need to be very forgiving for those who are not perfectly in-tune or accurate singers to be useful to untrained singers. Morris says the software is simple enough to run on a cell phone.

Art

Predicting Stress - Sydney Morning Herald, April 17, 2008: University of Wisconsin-Madison professor Vadim Shapiro and his colleagues have developed Scan and Solve, software that can determine the stress on an object based only on its shape, which could help experts preserve pieces of artwork or help treat people's physical problems. The software was used on Michelangelo's David and determined the statue was under a significant amount of stress, particularly around its left thigh, right shin, and ankles. Scan and Solve's conclusions match the real cracks that have started to appear in the marble sculpture. The program could help archivists predict what areas of an ancient artifact may need to be reinforced to prevent damage, even if the statue has not yet shown any signs of stress or damage. "Understanding structural properties of historical and cultural artifacts through computer simulations is often crucial to their preservation," Shapiro says. The software converts a 3D map of an object into a map of the stresses and strains it will experience when subject to certain forces. Although the concept is not new, Shapiro's software simplifies the process and eliminates a series of difficult, error-prone calculations. Traditional computer simulations use a finite element analysis, which breaks the object into a 3D mesh of tiny pieces that approximate the shape. Shapiro's approach runs the analysis directly on the 3D shape data. Shapiro says the technique could also be used on scans of living bones in patients, for example by suggesting the best shape for hip bone replacements.