THE FOURTH PARADIGM IN PRACTICE PAGE 1 PAGE PAGE 2 3 PAGE PAGE 4 5 Science@Microsoft THE FOURTH PARADIGM IN PRACTICE © 2012 Microsoft Corporation. All rights reserved. Except where otherwise noted, content in this publication is licensed under the Creative Commons Attribution 3.0 United States license, available at www.creativecommons.org/licenses/by/3.0/legalcode. ISBN 978-0-9825442-1-1 Printed in the United States of America The information, findings, views, and opinions contained in this publication are those of the authors and do not necessarily reflect the views of Microsoft Corporation or Microsoft Research. Microsoft Corporation does not guarantee the accuracy of any information provided herein. Microsoft Research PAGE PAGE 6 7 Foreword IN THE 20 YEARS since its founding, Microsoft been making in a number of disciplines—from Research has grown from a small group of neurology and immunology to astronomy and climate researchers to more than 800 computer scientists and change—and describes the technologies that have researchers at labs on four continents. Throughout been deployed to gain these insights. We see our this growth, the mission of Microsoft Research has collaborative ventures and blue-sky research yielding remained consistent: to advance the state of the art returns both in the broader social arena and in in computer science and software engineering, and to improved products and services. It’s a classic case of take these technology advances to the public through “doing well by doing good.” our products. These stories also reveal interesting ways in which As in many areas of research, the eventual Microsoft and academic researchers are effectively applications and impact of computer-science applying computer science and technical computing research are challenging to predict and frequently research to fields far removed from computer science. different than originally envisioned. Over the years, With such multidisciplinary research collaborations, we have seen many instances where Microsoft Microsoft Research is helping researchers reduce researchers have made advances that are at first their time to new insights and accelerate the pace of incorporated into our products and technologies, scientific discovery. Microsoft’s unparalleled corporate but subsequently found to be uniquely impactful support of basic research is fundamental to our for an unrelated purpose in a very different field. long-term vision of transforming society through Research at Microsoft helps drive forward the entire technology. frontier of computing—and thus enables scientists We have seen research on spam filters with machine to make significant progress on some of the major learning lead to a new approach to develop an HIV challenges facing society. That’s why we collaborate vaccine. We have seen fundamental advances in with leading academic researchers around the world computer vision and speech processing research on a broad range of issues related to health, the lead to the Kinect hands-free controller. What will environment, education, and many other disciplines. be the next breakthrough discovery, or cool new By working on these non-computer-science projects product? Who can say? That’s the beauty of doing we often discover new ways to hone and improve our basic research: you’re never certain where the results own technologies—these are powerfully symbiotic might lead, but you can be sure the journey will be relationships. worthwhile and full of surprises. CRAIG MUNDIE Chief Research and Strategy Officer This collection of Science@Microsoft vignettes —CRAIG MUNDIE Microsoft Corporation illustrates some of the progress researchers have Chief Research and Strategy Officer PAGE PAGE 8 9 Table of Contents Genomics and Machine Learning Health and Computer Vision Using Model-Based Machine Learning to Understanding the Immune Response to HIV 16 Understand Childhood Asthma 38 Natural-killer cells play a direct role in fighting HIV Understanding childhood asthma Medical Sensing via a Contact Lens Understanding the Genetic Causes of Human 40 How this noninvasive technology monitors blood sugar levels 18 Disease Improving Echocardiography How researchers are untangling the complexity of human diseases 42 How scientists are improving the efficacy of echocardiography Algorithms that Can Handle the “Omics” Searching the Human Body 20 New developments in data analysis help address significant How researchers are untangling the complexity of human diseases problems in biological research 44 Identifying Genetic Factors in Disease with Big Data Computer Science and Technology 22 Analysis of large datasets helps researchers understand connections between heredity and disease SenseCam 48 This device can aid those with debilitating memory impairment Earth and Environment Technology to Combat Counterfeit Products 50 How science is protecting consumers from purchasing fraudulent Amassing Global Data on Carbon and Climate goods 26 Enabling scientists to investigate the biological implications of persistent weather events Clinical Studies and Data Collection and Reuse 52 How software can help make clinical studies more effective Simulating the Breathing of the Biosphere 28 Scientists address both the science and computational challenges Microsoft TerraServer: an Imagery Scalability Story 54 Online, high-resolution maps Data Deluge and Digital Watersheds 30 Using data to restore habitat for endangered fish Improving Fuel Refining Technologies 32 How computer vision research can transform MRI Table of contents continued next page ... Transforming the Science of Behavioral Ecology 34 Exploring novel ways of investigating wildlife species PAGE PAGE 10 11 Table of Contents Physics and Astronomy Citizen Science WorldWide Telescope and Seamless Astronomy GalaxyZoo 58 How scientists are interacting with the universe 76 How volunteers are assisting professional astronomers to classify galaxies SkyServer: the Universe at Your Fingertips 60 How software can help make clinical studies more effective Weatherathome.net Anyone in the world can run a regional climate model Topological Quantum Computation 78 62 Faster, more powerful, more versatile computing Rosetta@Home 80 Computer power—citizen participants help predict and design the three-dimensional structures Biology and Life Sciences Coevolution of Viruses and the Immune System Scientific Tools 66 Understanding the human body’s response to disease-causing pathogens Chemistry Add-in for Word Modify and share chemical information Software Verification Meets Biology 84 68 Biological models are bettering our understanding of biological NodeXL phenomena 86 NodeXL helps analyze and visualize its influence on individuals and societies Programming Life 70 Using genetic devices to reprogram cell behavior and improve health, Scientific Workflow Workbench agriculture, and energy 88 Modify and share chemical information How Many Species Are There? 72 Scientists are using expertise, tools, and technologies to find out PAGE PAGE 12 13 Genomics and Machine Learning PAGE PAGE 14 15 Genomics and Machine Learning “It is very exciting to take ideas from a Using Model-Based Machine Learning technology context and apply them to such an important societal problem. At the same to Understand Childhood Asthma time, the challenges of modeling a disease as complex as asthma are pushing us to develop ASTHMA AND ALLergies rank among the most box machine-learning methods, easily allows the machine-learning techniques in new common chronic disorders in children—and their the incorporation of rich, hierarchical structure directions.” —CHRIS BISHOP incidence is on the rise. The question is why. derived from clinical background knowledge. Understanding the underlying causes of asthma The project is a collaboration between Microsoft might lead to prevention in susceptible children Research and the University of Manchester. “With Microsoft Research, we have created a and better treatment for adults. Microsoft Research provides the machine- multi-disciplinary collaborative partnership Although evidence from twin studies suggests learning expertise through its team of Chris which will combine our world-leading expertise a strong genetic component in asthma and Bishop, John Winn, Markus Svensén, and Nevena in birth cohorts and health informatics allergies, few of these studies have identified the Lazic in the Machine Learning and Perception same genetic associations. Moreover, the role group, and has contributed Infer.NET, a new research with innovative computational of the environment in asthma and allergies is framework that allows rapid construction of statistical methods. We will work together to evidenced by the rapid increase in the prevalence complex Bayesian models and performs efficient apply newly developed state-of-the-art data of these disorders over the last four to five inference within those models. The University of decades, a time frame too short to be attributable Manchester brings world-class clinical expertise analysis techniques (of Bayesian inference to genetic factors alone. And indeed, various through Iain Buchan, Adnan Custovic, and Angela and machine learning) to build complex models environmental exposures have been associated Simpson, along with a high-quality dataset to describe different types of ‘asthma’ and with the development of asthma and allergies. collected by the Manchester Asthma and Allergies investigate risk factors (both genetic and However, as with genetics, the data on the role of Study. environment) for