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Accurate Protein Function Prediction Using the GOstruct Method
Abstract
With the exponential proliferation of sequenced genomes, performing
biological experiments for determining the function of genes and
proteins is not practical. Accurate prediction of protein function is
therefore of great importance. And yet the basic methodology employed
by genome annotators has remained unchanged for a long time. The
system of keywords used to describe protein function is the Gene
Ontology (GO), which provides thousands of keywords arranged in a
hierarchy of increasing specificity. The large number of keywords and
the hierarchical structure of the annotation space make this a
challenging learning problem. In this talk I will formulate the
problem of Gene Ontology term prediction as a hierarchical
classification problem and present the GOstruct method for addressing
it. The GOstruct method, which is based on the framework of kernel
methods for structured output spaces, will be shown to outperform
existing approaches.
Detecting Service Violation in Internet and Mobile Ad Hoc Networks
Abstract
Networks are vulnerable to attacks from users and malicious hosts.
For the internet, we present monitoring schemes based on low cost
probes that use only edge to edge measurements. These schemes are
scalable in large network domains. Stripes and overlay-based schemes
are used to infer delay and loss at egress routers and detect
congestions and misbehaved flows due to Service Level Agreement (SLA)
violations. Experimental study measures overheads, delays, loss ratio,
accuracy, and convergence time. Research results provide guidelines
that allow in integrating schemes that can deal with intrusions and
preserve QoS. Filters at ingress routers are used to block violating
flows. In ad hoc networks, malicious attackers can prevent the
integrity of the route establishment. The research challenge is to
identify and isolate the attackers. The malicious hosts may be
included in suspicious lists or blacklists depending upon trust and
global information. Experimental studies measure effectiveness,
accuracy, overhead, and throughput of a Reverse Labeling Restriction
(RLR).
Wormhole attacks, authentication, and privacy research will be briefly
presented. This talk is based on joint work with A. Habib, Y. Lu, and
W. Wang.
Biography
Bharat Bhargava is a professor of the Department of Computer Science
with a courtesy appointment in the School of Electrical & Computer
Engineering at Purdue University. Professor Bhargava is conducting
research in security and privacy issues in distributed systems. This
involves host authentication and key management, secure routing and
dealing with malicious hosts, adaptability to attacks, and
experimental studies. Related research is in formalizing evidence,
trust, and fraud. In the 1988 IEEE Data Engineering Conference, he and
John Riedl received the best paper award for their work on "A Model
for Adaptable Systems for Transaction Processing." Professor Bhargava
is a Fellow of the Institute of Electrical and Electronics Engineers
and of the Institute of Electronics and Telecommunication
Engineers. In 1999, he received the IEEE Technical Achievement Award
for a major impact of his decade long contributions to foundations of
adaptability in communication and distributed systems. He has been
awarded the charter Gold Core Member distinction by the IEEE Computer
Society for his distinguished service. He received Outstanding
Instructor Awards from the Purdue chapter of the ACM in 1996 and
1998. In 2003, he was inducted in the Purdue's Book of Great
Teachers. He also served the IEEE Computer Society on Technical
Achievement award and Fellow committees. Professor Bhargava is the
founder of the IEEE Symposium on Reliable and Distributed Systems.
Cloud Computing: A Survey of Causative Forces, Models and Challenges
Abstract
Cloud computing harnesses the compute and storage capabilities available in
vast data centers. In this talk we will look at some of the forces that
underlie the shift towards cloud computing. Data centers rely on commodity
components which, in turn, impacts reliability. We will review the
implications of this choice on how file systems are designed and also on how
structured data is managed. The most dominant model for cloud computing is
the MapReduce framework; we will look at how this simplifies, and can
constrain, application development. We will also look at some of the
implications - economic, environmental and privacy issues - of moving into
the cloud.
Brief Biography
Shrideep Pallickara is an Assistant Professor in the Department of Computer
Science at Colorado State University. He conducts research in the area of
large-scale systems; specifically, cloud computing and streaming systems. He
is the creator of two systems: NaradaBrokering - for the dissemination of
voluminous streams, and Granules - a lightweight runtime for cloud
computing.
The Rise and Fall of Systems Engineering
Abstract
As solutions to technological challenges have become more and more
complex exploding demand has been created for engineers possessing the
breadth of knowledge to address systems issues. One of the attributes
of good systems engineers is, unfortunately, the prior accumulation of
scar tissue. This lecture seeks to provide the listener with "virtual"
scar tissue, based upon the lessons learned by the speaker during
nearly a half-century career.
Brief Biography
Norman R. Augustine's distinguished career in the science and
technology arena has included prominent positions in government,
industry, academia, and the nonprofit sector. He is widely known for
chairing the National Academies committee that produced the report
"Rising Above the Gathering Storm: Energizing and Employing America
for a Brighter Economic Future." Dr. Augustine has served as under
secretary and acting secretary of the Army, Chairman and CEO of Martin
Marietta Corporation and later of Lockheed Martin Corporation, and
professor at Princeton University. He has been chairman of the
National Academy of Engineering, the Defense Science Board, the
American Red Cross, and the Aerospace Industries Association, and was
a 16-year member of the President's Council of Advisors on Science and
Technology. He is a Regent of the University System of Maryland, a
former trustee of MIT and Princeton University, and a trustee emeritus
of Johns Hopkins. His honors include the National Medal of Technology
and the Vannevar Bush Award. He is a five-time recipient of the
Defense Department's Distinguished Service Medal and holds 23 honorary
degrees.
Photons at Work: From Silicon to DNA, and Back
Abstract
This talk will review the research activity in the area of
nanofabrication, covering a broad spectrum from semiconductor
technology to DNA-based fabrication. Recently lithography has been
extended to biological problems, in what can be termed Biological
Lithography. Lithographic techniques applied to biological problems
includes âgene synthesisâ process whereby the oligomers synthesized
are harvested from the surface, amplified and stepwise assembled in
longer constructs. âSynthetic genesâ can be used to encode biological
functions, or to enable the use of DNA as structural material. The
sequence of bases in DNA encodes the genetic information, but DNA
itself can be used as a âstructural buildingâ block where the sequence
information is used for "smart" assembly of structures of various
shapes.
Brief Biography
Dr. Franco Cerrina is
Professor and Chairman of Electrical and Computer Engineering, at
Boston University since 2008. Previously, he was the Lynn H. Matthias
Professor of Electrical and Computer Engineering at the University of
Wisconsin-Madison. He is an IEEE, APS, OSA, AAAS and SPIE Fellow,
recipient of the SRC Aristotle award, and has been the director of the
Center for NanoTechnology (University of Wisconsin at Madison) from
1988 to 2008.
His research work is centered on semiconductor fabrication, optical
patterning and advanced lithography. Multidisciplinary in nature, this
activity applied to the development of novel technologies, and to
their use in real-world engineering problems, including the
application of microfabrication techniques to biological and genomic
problems, ranging from DNA Microarrays, to DNA de-novo synthesis and
to the use of DNA in nanofabrication. He has developed a novel
Maskless photolithographic method for the rapid synthesis of DNA
microarray chips (MAS). In addition to his academic work, he has
successfully transferred several technologies to companies that he
founded. The MAS is commercialized by RocheâNimbleGen Systems, a
Madison (Wi) company of which he has been the first VP of
Engineering. He has also been a co-founder and CEO of Genetic
Assemblies, Inc., a company dedicated to the synthesis of long DNA
strands (synthetic genes). In 2008 he has cofounded BioLitho,
incorporated in Illinois, and in 2009 Gen9, a genomic company based in
Cambridge, Massachusetts.
Quantum Computing and Cellular Phones
Biography
Robert Calderbank is Professor of Electrical Engineering and
Mathematics at Princeton University where he directs the Program in
Applied and Computational Mathematics. He joined Princeton from AT&T
where he was Vice President for Research and responsible for designing
the first Research Lab in the world where the primary focus is data at
massive scale. Advances by Dr. Calderbank have transformed
communications practice in voiceband modems, advanced read channels
for magnetic recording, and wireless systems and have also opened the
door to fault tolerant quantum computation.
Prof. Calderbank is an IEEE Fellow and was honored by the IEEE
Information Theory Prize Paper Award in 1995 and again in 1999 He
was elected to the National Academy of Engineering in 2005.
Nathan McEachen
Abstract
The Model-Driven Architecture (MDA) approach allows a software system
to be specified by using a platform-independent model (PIM) with a
domain-specific language (DSL). The PIM can be used to automatically
generate a platform-specific model (PSM) that can execute on a target
platform. A PIM is a higher level of abstraction than a
general-purpose language like Java or C#. Using a PIM, developers can
spend more of their time architecting solutions and less time
implementing them. TerraFrame, Inc. has developed a software
development toolkit that is inspired by MDA to give software
developers the ability to rapidly build applications. Given a UML
class model, the entire technology stack of a web application can be
generated, compiled, and deployed at runtime.
Brief Biography
Nathan McEachen is the CTO and CEO of TerraFrame, Inc. He has nine
years of experience developing web applications that model complex
business domains such as B2B ecommerce and Product Lifecycle
Management. Nathan holds a B.S. in Computer Science from Cal Poly and
a M.S. in Computer Science from Colorado State University. He has
academic publications in testing Aspect-Oriented programs and
Aspect-Oriented Modeling.
Computational Thinking and Thinking About Computing
Abstract
My vision for the 21st Century: Computational thinking will be a
fundamental skill used by everyone in the world. To reading, writing,
and arithmetic, we should add computational thinking to every child's
analytical ability. Computational thinking involves solving problems,
designing systems, and understanding human behavior by drawing on the
concepts fundamental to computer science. Thinking like a computer
scientist means more than being able to program a computer. It
requires the ability to abstract and thus to think at multiple levels
of abstraction. In this talk I will argue that computational thinking
has already begun to influence other disciplines, and promote the idea
that teaching computational thinking can not only inspire future
generations to enter the field of computer science but also benefit
people in all fields.
In thinking about computing, I have started a list of "Deep Questions
in Computing," with the hope of encouraging the community to think
about the scientific drivers of our field. These drivers, alongside
technological innovation and societal grand challenges, point to a
bright future for computer science, with exciting new discoveries and
transformative capabilities yet to happen.
Brief Biography
Dr. Jeannette M. Wing is the President's Professor of Computer Science
in the Computer Science Department at Carnegie Mellon University. She
received her S.B. and S.M. degrees in Electrical Engineering and
Computer Science in 1979 and her Ph.D. degree in Computer Science in
1983, all from the Massachusetts Institute of Technology. From
2004-2007, she was Head of the Computer Science Department at Carnegie
Mellon. Currently on leave from CMU, she is the Assistant Director of
the Computer and Information Science and Engineering Directorate at
the National Science Foundation.
Professor Wing's general research interests are in the areas of
specification and verification, concurrent and distributed systems,
programming languages, and software engineering. Her current focus is
on the foundations of trustworthy computing. Professor Wing was or is
on the editorial board of twelve journals. She is a member of AAAS,
ACM, IEEE, Sigma Xi, Phi Beta Kappa, Tau Beta Pi, and Eta Kappa Nu,
and is an AAAS Fellow, ACM Fellow, and IEEE Fellow.
Kodu - End-user Programming and Design for Games
Abstract
Project Kodu is a kid-friendly game design and programming
environment which enables non-technical users to create complete
games - including "AI" behaviors - using only an XBox 360 controller
for input. Kodu includes a novel graphical programming environment
based on a concurrent rule system derived from contemporary robotics
practice. This language is approachable - it can be mastered by 10-
year-olds - yet expressive, and can be used to implement a broad
array of game genres. In addition to behavior editing, Kodu
integrates terrain and level design - providing a full-spectrum game
design system that is accessible to 9-year-olds (and their parents)
running on the XBox 360 or a Windows PC.
Kodu has been developed over two years in Microsoft Research in
collaboration with the XNA Team. It has been in pilots with children
as young as 9 for over a year and undergone hundreds of hours of
usability testing on both the user interface and the language
itself. In this talk, we'll provide an in-depth look at Kodu
including the design of the programming language, pilot programs
with Kodu in schools around the world, and the motivations of the
Project Kodu team at Microsoft Research.
Brief Biography
Matt MacLaurin is the instigator and leader of the Kodu project. As
Principal Program Manager in the Creative Systems team at Microsoft
Research, MacLaurin investigates the intersection of creativity,
entertainment, and social media, with a particular emphasis on how
sharing affects creativity and the different roles that form
naturally within online creative communities. Previously at
Microsoft, MacLaurin ran a team within the Windows organization
responsible for key innovations in user interface, search, and
animation in the Windows Shell for Vista and Windows 7.
Prior to Microsoft, MacLaurin worked as a senior engineer /
scientist at Apple Computer where he studied advanced interactive
media authoring environments, invented a new formal grammar for user
interface, and wrote the user interface framework for the Dylan-
based version of Newton - one of the first consumer-focused
operating systems written in managed code.
Between Apple and Microsoft, MacLaurin founded and ran a successful
interactive media consulting agency conducting advanced research and
product development for clients such as New Line Cinema, Apple,
Creative Systems, MCA, Silicon Graphics, Thorne EMI, Paramount,
Dreamworks, Capitol Records and Virgin Interactive, including the
brand introduction campaign for Mac OS, the first large-scale social
media systems for the music industry, and advanced character
animation systems for 3D environments. He is named as an inventor on
over 60 patent filings.
GIScience: Geographical Information Systems at CSU
Abstract
Geographic information science (GIS) is at the core of spatial
research activities that cross disciplinary boundaries. GIS explores
the fundamental theories and concepts that form geospatial
technologies (such as geographic information systems, remote sensing,
and global positioning systems) as well as application-based products
and activities. CSU hosts many researchers actively involved in a
variety of applications of GIS research. This seminar is a panel
discussion by several GIS faculty researchers at CSU: Luis Garcia,
Civil and Environmental Engineering; Dave Theobald, Human Dimensions
of Natural Resources; Raj Khosla, Soil and Crop Sciences; and Randy
Boone, Natural Resource Ecology Lab. Melinda Laituri, Forest,
Rangeland, and Watershed Stewardship, will moderate the panel. The
discussion will focus on current GIS research at CSU, its contribution
to computer-based methods and techniques, and future directions. This
panel will provide a springboard for the planned ISTeC Research
Retreat on Computing for GIS Problem Domains to be held on February 8,
2010.
Brief Biography
Dr. Laituri is at Colorado State University in the Forest, Rangeland,
and Watershed Stewardship Department. She is coordinating the
Geospatial Centroid @ CSU to provide information and communication
about GIS across campus. Dr. Laituri teaches graduate courses in
GIS. Her research focuses on the intersection of science and culture
using geospatial science. She has research projects in Mongolia, New
Zealand, Ethiopia, Canada, and China. Other research work focuses on
the role of the Internet and geospatial technologies of disaster
management and cross-cultural environmental histories of river basin
management.
Convex Subspace Routing: A Novel Virtual Coordinates Based
Routing Protocol for Sensor Networks
Abstract
Virtual Coordinate based Routing (VCR) is a class of simple scalable
routing schemes for sensor networks. VCR relies on coordinates based
on the number of hops to a set of anchors, rather than on geographical
coordinates. Multiple nodes with identical coordinates and local
minima encountered during routing degrade the performance of
VCR. Properties of virtual coordinate systems are analyzed to provide
insight into the nature of virtual coordinate space, and bounds are
derived for path lengths. A new routing scheme, Convex Subspace
Routing (CSR), is proposed. In contrast to existing VCR schemes that
use backtracking or hill climbing techniques to overcome local minima,
CSR avoids using anchors that cause local minima. CSR selects subsets
of anchors dynamically to provide a convex distance function from
source to destination. Consequently, it is less sensitive to anchor
placement and over anchoring, and does not require tracking of route
history for backtracking. Performance of CSR is evaluated for
different network configurations. Results for varying node densities
and different numbers of anchors indicate that CSR significantly
outperforms Logical Coordinate Routing (LCR), in terms of routability,
number of hops used for routing, memory usage as well as energy
consumption.
Asa Ben-Hur
Department of Computer Science
Colorado State University
Bharat
Bhargava
Department of Computer Science
Purdue University
Shrideep
Pallickara
Department of Computer Science
Colorado State University
Norman R. Augustine
Retired Chairman and CEO
Lockheed Martin Corporation
Franco Cerrina
Chair, Department of Electrical and Computer Engineering
Boston University
Robert Calderbank
Professor of Electrical Engineering, Mathematics and Applied and
Computational Mathematics
Princeton University
TerraFrame, co-founder, CTO & Interim CEO
Model-Driven Architecture (MDA) in Practice
Dr. Jeanette Wing
NSF Assistant Director of the Computer and Information Science and
Engineering Directorate
Carnegie Mellon University
President's Professor of Computer Science
Matt MacLaurin
Principal Program Manager
Creative Systems Group
Microsoft Research
Melinda Laituri
Dept. of Forest, Rangeland, and Watershed Stewardship
Colorado State University
Dulanjalie Dhanapala
Department of Electrical and Computer Engineering
Colorado State University