Archive for the ‘Gaming’ Category
The gamification of data analysis in cancer increases citizen contribution and reduces research time
Individuals diagnosed with muscle-invasive bladder cancer face a difficult treatment decision – intensive radiotherapy or complete surgical removal of their bladder. Each option has benefits and draw backs, and there are limited data available to patients and physicians to help predict which treatment might provide the best outcome.
Dr. Anne Kiltie, Associate Professor of Radiation Oncology at Oxford University and Clinical Group Leader at Cancer Research UK (CRUK) is trying to improve that decision making process. She is investigating whether proteins involved in DNA damage signaling and repair might serve as biological indicators, or ‘biomarkers’, predictive of a patient’s response to treatment.
In 2010 her team published data showing that higher levels of the DNA repair protein MRE11 correlated with better survival rates in bladder cancer patients who had undergone radiotherapy. This was a critical finding suggesting that MRE11 could be a treatment predictive biomarker. Unfortunately the finding relied on time consuming pathology analysis. Bladder tumor samples are sliced, labeled for each protein of interest and photographed. While the staining and imaging of these slices can be automated, each image must be manually quantified for the level of protein present. Computer algorithms are not yet as reliable as the human eye. So to study just one protein, Kiltie’s team must individually score hundreds of images, a major time sink.
Of course if there was a way to get more people involved, the research could proceed much faster.
And this is the basis of Reverse the Odds, a mobile app game in which citizens help with real data analysis. The game was the result of CRUK’s partnership with British television broadcaster Channel 4 and developed in collaboration with Chunk, Maverick Television, and Zooniverse.
“Developing this game was a new experience for both our researchers and the game developers,” says Rupesh Robinson-Vyas, Science Engagement and Operations Officer at CRUK. The development team had some key concerns. Could a game that dealt with a serious topic like cancer still be approachable and fun? And could the data analysis be gamified without compromising the quality of analysis?
Yes and yes.
The final product is a puzzle game in which players help whimsical creatures, ‘Odds’ reclaim their world. Rather than hide the science, the game developers put the science front and center. To level up, players visit the ‘lab’ where they learn to quantify protein expression in real bladder tumor samples. All the samples are from patients who have already undergone treatment. Players are not diagnosing patients.
Each image is reviewed by multiple players, with each player’s response being compared to other players’ responses. In this way discrepancies in analysis are weeded out. After the images are quantified, the data are sent back to Kiltie’s team who compare the level of protein expression to the patient’s known outcome.
Not only has the game cut down on data processing time, Kiltie’s team can concurrently evaluate the expression level of multiple proteins. This means the relationships between proteins, how they might work together to affect treatment outcome can also be studied.
As for the seriousness of the subject matter, rather than a deterrent, the science and the potential to make a significant contribution to cancer research is a strong motivator for game play.
“It was an unexpected outcome. The game allowed us to engage a younger age group, individuals who might not be able to contribute financially, could instead contribute their time,” says Robinson-Vyas. The game has been a huge success, translated into five languages, with an international reach of 150 countries.
CRUK is testing new methods of training and presenting pathology data to users. “Rather than asking our users just one question, the new interactive will teach us how to ask questions and identify what kind of data our users can help us collect,” says Robinson-Vyas. Results with citizen scientists matching pathologist’s accuracy in data analysis are encouraging; CRUK is writing a paper on these methods and plans to test further iterations.
As for Reverse the Odds, Kiltie’s team hopes to complete data collection this spring. Her team intends to make the results as well as background on game development openly available.
Visit the project page to learn more about Reverse the Odds and join the effort help Kiltie’s team analyze the final 500,000 slides by March.
Learn about CRUK’s other project Play to Cure: Genes in Space
With our ever-increasing connectivity and reliance on the internet, cybersecurity is a growing concern. Despite all the cautionary warnings about cyber safety, individuals, companies and government agencies still fall victim to attack.
So what does it take to stay safe? NOVA, in partnership with computer scientists and cybersecurity experts, created the Cybersecurity Lab, a digital platform designed to teach people about cyber threats and how to improve their own cybersecurity. Read the rest of this entry »
VerbCorner invites citizen scientists to answer fun questions about words and their meanings to eventually help train computers to understand language.
SciStarter is shuffling science into the language department. Explore the science of words with these citizen science projects!
Verb. Noun. Pronoun. Adjective. Adverb. Preposition. Conjunction. Interjection… If you’re anything like me, the sight of sentence diagrams and parts of speech trigger nightmares of grade school English class and number 2 pencils. But, how do we understand what a word means? As useful as dictionaries are, they only provide other words in their definitions. How do we know when to use one word in a sentence and not another? How do we explain a complex idea to children?
In July 2013, Lily Bui introduced us to VerbCorner, a citizen science project investigating the structure of language and, ultimately, the structure of thought. According to Dr. Hartshorne, the director of MIT’s Games With Words, “Scientists still haven’t worked out the exact meaning of most words… It is [similarly] hard to understand how children come to learn the meanings of words, when we don’t fully understand those meanings ourselves… I can tell you as a former translator, we translate words into meaning and then back into words.” With an infinite number of words and sentence structures, where should linguists begin to understand their meanings?
In VerbCorner, the mammoth task of understanding how language is structured is broken down into smaller, simple tasks. Through wild stories, each task focuses on one of seven unique aspects of verb meaning to elucidate the fundamental building blocks scientists think make up language such as how a verb is used and its relationship to a change of state. To date, over 1500 citizen scientists have provided more than 117,000 judgments on the initial 641 chosen verbs and six aspects of meaning, supplying Dr. Hartshorne and colleagues enough preliminary data to begin understanding how we understand words.
Are there patterns to how we use verbs? Do we systematically choose words? Or is our word choice completely random and learned in childhood? Regardless of what language you speak, scientists are learning that how we choose words appears to be similar. Scientists have discovered there is a relationship between grammar and meaning which is systematic, and thereby machine learnable. Previous work by Beth Levin lead to the creation of VerbNet, a database where verbs are categorized based on their meaning and usage. Citizen scientists in VerbCorner are helping Dr. Hartshorne’s team verify that verbs with similar descriptions (such as contact or force) are similarly classified and only work in particular grammatical situations.
According to Dr. Hartshorne, “The most interesting things we are learning are about the building blocks of the mind.” In the initial release of VerbCorner, one task tried to understand the building block ‘change of state’ be it physical, mental, or a location. “If ‘change of state’ really was a core component of how we conceptualize the world, it should have been easy to make a task that got at it. We were unable to make such a task. People found it very hard to keep track of all three types of changes.” Dr. Hartshorne explained. Consequently, the initial task was broken down into three new tasks, each focusing on a different aspect of changing state. Suddenly, citizen scientists were able to complete the task. “This suggests that linguists were wrong about ‘change of state’ being a building block of meaning… Rather the building blocks are probably ‘change of physical state’, ‘change of location’, ‘change of mental state’, and possibly more.”
With these results, VerbCorner achieved its first goal – the analysis of the original 641 verbs and six aspects of meaning. But, there is lots of work still to do – another 400 verbs and four additional tasks have recently been added to the project which ultimately plans to cover all the verbs and components of meaning in VerbNet. Linguists, psychologists, and computer scientists plan to use our evolving understand of language and meaning to develop a deeper understanding of human thought as well as fine tune the artificial intelligence programming society is increasingly reliant upon.
Why not flex your mind over language skills at VerbCorner this afternoon? I’m certain you know more than Siri.
Dr. Melinda T. Hough is a freelance science advocate and communicator. Her previous work has included a Mirzayan Science and Technology Graduate Policy Fellowship at the National Academy of Sciences (2012), co-development of several of the final science policy questions with ScienceDebate.org (2012), consulting on the development of the Seattle Science Festival EXPO day (2012), contributing photographer for JF Derry’s book “Darwin in Scotland” (2010) and outreach projects to numerous to count. Not content to stay stateside, Melinda received a B.S in Microbiology from the University of Washington (2001) before moving to Edinburgh, Scotland where she received a MSc (2002) and PhD (2008) from the University of Edinburgh trying to understand how antibiotics kill bacteria. Naturally curious, it is hard to tear Melinda away from science; but if you can, she might be found exploring, often behind the lens of her Nikon D80, training for two half-marathons, or plotting her next epic adventure.