Mingfu Shao

Laboratory of Computational Biology and Bioinformatics Ecole Polytechnique Federale de Lausanne COLLOQUIUM Date: March 28, 2014 Time: 1400-1500 (2:00pm-3:00pm) Place: Swearingen 2A15 Abstract A basic problem in comparative genomics is to compute the edit distance between two genomes, i.e., the minimum number of large-scale evolutionary events that can transform one genome into the other. These evolutionary events fall into two categories: rearrangements and content-modifying operations. Most of the genomic rearrangements events can be modelled by the double-cut-and-join (DCJ) operation, which has formed the basis for much algorithmic research on rearrangements over the last few years. Content-modifying operations include insertions, deletions, and segmental duplications. In this talk, we first discuss the edit distance in terms of DCJ operations and segmental duplications. A new graphical data structure, the trajectory graph, is introduced to model and possibly refine any given evolutionary trajectory between two genomes. We then show how to compute the edit distance between genomes in the presence of duplicate genes. We formulate it as an integer linear programming problem and provide an efficient preprocessing approach while preserving optimality. To the best of our knowledge, this is the first practical approach to compute the exact edit distance between genomes with duplicated genes, which also results in more accurate assignments of orthologs between genomes than state-of-the-art methods. Mingfu Shao is a third-year Ph.D student in the Laboratory of Computational Biology and Bioinformatics, École Polytechnique Fédérale de Lausanne (EPFL), Switzerland. His research interests focus on comparative genomes, especially designing algorithms for problems arising in genomic rearrangements and phylogeny construction. Mingfu received his BS degree from the Institute of Beijing Technology, and his MS degree from the Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China

Hongyiung Du

PhD Defense

Abstract

Complex resource allocation problems arise due to complex human societies and scarce resources to be distributed. Scarce resources could be food, water, energy, etc. Meanwhile, the size of the problem, the intersection of different areas, and possible global consequences all add to the complexity of the problems, which makes it difficult for humans to solve the problems by themselves. For all these reasons, humans need technical help to tackle complex problems. Since humans participated in the problems usually own part of the information about the problems, and no one may see the whole picture of the problems, it is natural to use distributed systems to simulate and analyze the problems. In a distributed system, humans represented by agents know only partial information interact with each other in order to achieve a common goal while maximizing their own interests. The formed distributed system is called a multiagent system because multiple agents are involved in the systems. In this dissertation, we studied three cases of multiagent systems to help with distributing a certain kind of resource. First we present an approach to assist grocery shopping. The aim is to help a customer to find the most economical way of shopping. A customer would save 21% or more most of the time with simulated price data and 6.7% with real price data. Robustness is also considered with deceptive stores and wrongly reported prices. Second we simulate a healthcare system in which agents are used to assist a patient to find a physician. We investigate four different strategies for assisting a person in choosing a physician and three physician-waiting policies in three common social network models. The results show that the sociotechnical system can decrease the number of annual sick days per person by 0.42-1.84 days compared with choosing a physician randomly. Third we investigate the influence of humans' personalities on resource allocation in mixed human-agent societies. It is shown that humans treat other humans and agents differently and humans with different temperaments behave differently, but not with significantly difference, which means fair is more important than personality types while making decisions.

COLLOQUIUM Department of Computer Science and Engineering University of South Carolina Kirk Cameron Department of Computer Science Virginia Polytechnic Institute and State University Date: March 17, 2014 Time: 1345-1445 (1:45pm-2:45pm) Place: Swearingen 1A03 (Faculty Lounge) Abstract Green High Performance Computing (HPC) is an oxymoron. How can something be “green” when it consumes over 10 megawatts of power? Utility companies pay customers to use less power. Seriously. Energy use per capita continues to increase worldwide yet most agree new power production facilities should not be built in their backyards. HPC cannot operate in a vacuum. Whether we like it or not, we are part of a large multi-market ecosystem at the intersection of the commodity markets for advanced computer hardware and the energy markets for power. This talk will provide a historical view of the Green HPC movement including some of my own power-aware software successes and failures. I’ll discuss the challenges facing computer energy efficiency research and how market forces will likely affect big changes in the future of HPC. Kirk W. Cameron is a Professor of Computer Science and Faculty Fellow at Virginia Tech. He works to improve performance and power efficiency in high performance computing (HPC) systems and applications. Prior to joining VT, he was an assistant professor of Computer Science and Engineering at the University of South Carolina from 2001-2005. Prof. Cameron is an award-winning pioneer of Green HPC. He co-founded the Green500 List and SPEC Power. His startup company MiserWare created the world's most popular free energy management software with half a million users in 160+ countries

USC's first ever Coda-A-Thon will be an opportunity for you and the members of your team to demonstrate your prowess in software development. You will have just 18 hours to solve a programming challenge that the faculty in the Department of Computer Science and Engineering will devise. Results are what counts, so you will be able to use the platform of your choice. Register and More Information Here.

This Talk has been postponed due to inclement weather.

Nancy Amato ACM Distinguished Speaker Based in TX, USA COLLOQUIUM Department of Computer Science and Engineering University of South Carolina Sampling-Based Motion Planning: From Intelligent CAD to Crowd Simulation to Protein Folding Nancy Amato Department of Computer Science and Engineering Texas A&M University Date: February 11, 2014 Time: 1700-1800 (4:00pm-5:00pm) Place: Swearingen 1A03 (Faculty Lounge) Abstract Motion planning arises in many application domains such as computer animation (digital actors), mixed reality systems and intelligent CAD (virtual prototyping and training), and even computational biology and chemistry (protein folding and drug design). Surprisingly, one type of sampling-based planner, the probabilistic roadmap method (PRM), has proven effective on problems from all these domains. In this talk, we describe the PRM framework and give an overview of some PRM variants developed in our group. We describe in more detail our work related to virtual prototyping, crowd simulation, and protein folding. For virtual prototyping, we show that in some cases a hybrid system incorporating both an automatic planner and haptic user input leads to superior results. For crowd simulation, we describe PRM-based techniques for pursuit evasion, evacuation planning and architectural design. Finally, we describe our application of PRMs to simulate molecular motions, such as protein and RNA folding. More information regarding our work, including movies, can be found at http://parasol.tamu.edu/~amato/. Nancy M. Amato is Unocal Professor and Interim Department Head of the Department of Computer Science and Engineering at Texas A&M University where she co-directs the Parasol Lab. Her main areas of research focus are motion planning and robotics, computational biology and geometry, and parallel and distributed computing. She received undergraduate degrees in Mathematical Sciences and Economics from Stanford University, and M.S. and Ph.D. degrees in Computer Science from UC Berkeley and the University of Illinois at Urbana-Champaign, respectively. She was an AT&T Bell Laboratories PhD Scholar, received an NSF CAREER Award, is a Distinguished Speaker for the ACM Distinguished Speakers Program, and was a Distinguished Lecturer for the IEEE Robotics and Automation Society. She served as the Editor-in-Chief of the IEEE/RSJ IROS Conference Paper Review Board and will be program chair for IEEE ICRA 2015. She was co-Chair of the National Center for Women in Information Technology (NCWIT) Academic Alliance, and currently serves on the CRA-W, CRA-E, and CDC committees. She is a Fellow of the American Association for the Advancement of Science (AAAS), a Fellow of the Institute of Electrical and Electronics Engineers (IEEE), a Fellow of the World Technology Network (WTN). She served as the Editor-in-Chief of the IROS Conference Paper Review Board (2011-2013), as an Editor for the IEEE Robotics and Automation Society Conference Editorial Board (2006-2010), and as an Associate Editor for the IEEE Transactions on Robotics and Automation and of the IEEE Transactions on Parallel and Distributed Computing. She is an elected member of the IEEE Robotics and Automation Society Administrative Committee (AdCom), She was co-Chair of the National Center for Women in Information Technology (NCWIT) Academic Alliance (2009-2011), is a member of the Computing Research Association's Committees on the Status of Women in Computing Research (CRA-W) and Education (CRA-E), and of the Coalition to Diversity Computing (CDC). She has directed or co-directed the CRA-W/CDC Distributed Research Experiences for Undergraduates (DREU, formally known as the DMP) since 2000; DREU is a national program that matches undergraduate women and students from underrepresented groups, including ethnic minorities and persons with disabilities, with a faculty mentor for a summer research experience at the faculty member's home institution. Her main areas of research focus are motion planning and robotics, computational biology and geometry, and parallel and distributed computing. She has graduated 14 PhD students, with most of them going on to careers in academia (7) and government or industry research labs (5), 18 master's students, and has worked with more than 100 Texas A&M undergraduate researchers and non-Texas A&M student interns, with the majority being students from groups underrepresented in computing. She currently supervises 13 PhD students, 2 masters students, and more than 10 undergraduate and high school researchers.

I hope everyone had a great first week of classes! I know it is a little late, but we will be holding our first meeting of this semester tomorrow (Wednesday) at 6:30 pm in room 2A17. If a lot of people show up then we will probably move into 2A31, but if/when the time comes to move we will let everyone know. The general purpose behind this meeting is to introduce the new officers and discuss some of the events we have planned for this semester. Hope to see you all there! Jonathan - Chair Shawn - Vice Chair Lacie - Secretary Aadel - Treasurer Patrick - Memeber chair ACM.USC

To get all the details, click here.

About the Premier healthcare alliance: A Malcolm Baldrige National Quality Award recipient Premier, Inc. (NASDAQ: PINC) is one of the nation’s leading healthcare improvement companies, uniting 2,900 hospitals and more than 100,000 other providers of care to transform healthcare. These members use Premier’s integrated data, benchmarking analytics, collaboratives, consulting and other services to drive innovation in the healthcare supply chain, deliver continuous improvements in healthcare costs and quality, and support success under emerging population health models. Premier plays a critical role in the rapidly evolving healthcare industry, collaborating with members to co-develop long-term solutions that reinvent and improve the way care is delivered to patients nationwide. Headquartered in Charlotte, N.C., Premier is passionate about leading the transformation to coordinated, high-quality, cost-effective care. Additional information is available at www.premierinc.com. Come follow us: LinkedIn - Facebook - Twitter - YouTube. About the Internship Program: Over a twelve week period students become a contributing member of the team working on meaningful projects that provide an opportunity to build their resume and have measurable success on key deliverables. Each student is paired with a Supervisor and Mentor to guide their professional development through the summer. In addition to exposure within their department, students will have ongoing lunch and learns, community and social events to learn more about Premier, the healthcare industry and the Charlotte area.

COLLOQUIUM Department of Computer Science and Engineering University of South Carolina Research Roadmap Driven by Network Benchmarking Lab (NBL): Deep Packet Inspection, Traffic Forensics, WLAN/LTE, Embedded Benchmarking, and Beyond Ying-Dar Lin Department of Computer Science National Chiao Tung University Abstract Most researchers look for topics from the literature. But our research has been driven mostly by development, which in turn has been driven by industrial projects or lab works. We first compare three different sources of research topics. We then derive two research tracks driven by product development and product testing, named the blue track and the green track, respectively. Each track is further divided into a development plane and a research plane. The blue track on product development has fostered a startup company (L7 Networks Inc.) and a textbook (Computer Networks: An Open Source Approach, McGraw-Hill 2011) at the development plane and also a research roadmap on QoS and deep packet inspection (DPI) at the research plane. On the other hand, the green track on product testing has triggered a 3rd-party test bed, Network Benchmarking Lab (NBL, www.nbl.org.tw), at the development plane and a research roadmap on traffic forensics, WLAN/LTE, and embedded benchmarking at the research plane. Throughout this talk, we illustrate how development and research could be highly interleaved. At the end, we give lessons accumulated over the past decade. The audience will see how research could be conducted in a different way. Ying-Dar Lin is Professor of Computer Science at National Chiao Tung University (NCTU) in Taiwan. He received his Ph.D. in Computer Science from UCLA in 1993. He served as the CEO of Telecom Technology Center during 2010-2011 and as a visiting scholar at Cisco Systems in San Jose during 2007–2008. Since 2002, he has been the founding director of Network Benchmarking Lab (NBL, www.nbl.org.tw), which reviews network products with real traffic. He also cofounded L7 Networks Inc. in 2002, which was later acquired by D-Link Corp. He founded Embedded Benchmarking Lab (www.ebl.org.tw) in 2011 to extend into the review of handheld devices. His research interests include design, analysis, implementation, and benchmarking of network protocols and algorithms, quality of services, network security, deep packet inspection, P2P networking, and embedded hardware/software co-design. His work on “multi-hop cellular” was the first along this line, and has been cited over 600 times and standardized into IEEE 802.11s, WiMAX IEEE 802.16j, and 3GPP LTE-Advanced. He was elevated to IEEE Fellow in 2013 for his contributions to multi-hop cellular communications and deep packet inspection. He is currently on the editorial boards of IEEE Transactions on Computers, IEEE Computer, IEEE Network, IEEE Communications Magazine - Network Testing Series, IEEE Wireless Communications, IEEE Communications Surveys and Tutorials, IEEE Communications Letters, Computer Communications, Computer Networks, and IEICE Transactions on Information and Systems. He published the textbook Computer Networks: An Open Source Approach (www.mhhe.com/lin), with Ren-Hung Hwang and Fred Baker (McGraw-Hill, 2011). It is the first text that interleaves open source implementation examples with protocol design descriptions to bridge the gap between design and implementation.