Seminars
** Extended Deadline **
Isaac Newton Institute for Mathematical Sciences, Cambridge, UK
EMBO Workshop on Current Challenges and Problems in Phylogenetics (3 September to 7 September 2007) in association with the Newton Institute programme entitled Phylogenetics (3 September to 21 December 2007)
Sponsored by: European Molecular Biology Organisation (EMBO)
Principal Organiser: Professor Vincent Moulton (University of East Anglia)
Organisers: Dr Brent Emerson (University of East Anglia), Professor Daniel Huson (Tuebingen University) and Professor Mike Steel (University of Canterbury)
Theme of Workshop: Phylogenetic trees and networks are central to modern molecular evolutionary biology, with applications ranging from the origin of viruses (e.g. HIV, influenza) to modelling plant and animal radiations. As biologists attempt to reconstruct larger slices of the ‘tree of life’ using increasingly complex data, and incorporating more accurate models of molecular evolution, mathematics (and its sister fields, statistics and computer science) is increasingly being seen as an essential tool.
This workshop will showcase some of the recent achievements, challenges and new problems that arise in using mathematical approaches to understand molecular evolution. Topics covered will include: phylogenomics, molecular epidemiology, genetic biodiversity and phylogeography, processes of reticulate evolution (such as horizontal gene transfer), haplotype mapping by perfect phylogeny, population genetics in phylogeny, and metagenomics.
In addition this workshop will launch (and set the agenda for) a 4-month workshop of collaboration and research at the Isaac Newton Institute for Mathematical Sciences in a program on Phylogenetics, which will bring mathematicians and biologists together to develop new approaches in molecular phylogenetics.
Invited Speakers: J Felsenstein (Washington), O Gascuel (LIRMM), J Hein (Oxford), J Kim (Pennsylvania), W Martin (Heinrich-Heine), A Mooers (Simon Fraser), L Pachter (UC Berkeley), A Rodrigo (Auckland), A von Haeseler (Duesseldorf) and T Warnow (Texas).
Location and Cost: The workshop will take place at the Newton Institute and accommodation for participants will be provided in a single study bedroom with shared bathroom at Wolfson Court. The workshop package, costing 450GBP, includes accommodation, breakfast and dinner from dinner on Sunday 2 September to breakfast on Saturday 8 September 2007, and lunch and refreshments during the days that lectures take place. Participants who wish to attend but do not require the workshop package will be charged a registration fee of 90GBP. Self-supporting participants are very welcome to apply.
Further Information and Application Forms are available from the WWW at:
<http://www.newton.cam.ac.uk/programmes/PLG/plgw01.html>
** Closing Date for the receipt of applications is 30 June 2007 **
************************************************************
Tracey Andrew
Programme and Visitor Officer
Isaac Newton Institute
20 Clarkson Road
Cambridge
CB3 0EH
UK
Tel: + 44 1223 335984
Fax: + 44 1223 330508
http://www.newton.cam.ac.uk/
UTCS Colloquium/EDGE Seminar
Michel Raynal /IRISA-CNRS-INRIA-University, Rennes, France
Wednesday, June 6, 2007 11:00 a.m. - 12:30 p.m. - ACES 3.408
Host: Prof. Vijay Garg
"The Notion of a Timed Register and its Application to IndulgentSynchronization"
Talk Abstract:
A new type of shared object, called "timed register", is proposed and used for the design of indulgent timing-based algorithms. A timed register generalizes the notion of an atomic register as follows: if a process invokes two consecutive operations on the same timed register which are a read followed by a write, then the write operation is executed only if it is invoked at most d time units after the read operation, where d is defined as part of the read operation. In this context, a timing-based algorithm is an algorithm whose correctness relies on the existence of a bound Delta such that any pair of consecutive constrained read and write operations issued by the same process on the same timed register are separated by at most Delta time units. An indulgent algorithm is an algorithm that always guarantees the safety properties, and ensures the liveness property as soon as the timing assumptions are satisfied. The usefulness of this new type of shared object is demonstrated by presenting simple and elegant indulgent timing-based algorithms that solve the mutual exclusion, L-exclusion, adaptive renaming, test&set, and consensus problems. Interestingly, timed registers are universal objects in systems with process crashes and transient timing failures (i.e., they allow building any concurrent object with a sequential specification).
Speaker Bio:
Michel Raynal (http://www.irisa.fr/michel.raynal/)has been a professor of computer science since 1981. At IRISA (CNRS-INRIA-University joint computing research laboratory located in Rennes), he founded a research group on Distributed Algorithms in 1983. His research interests include distributed algorithms, distributed computing systems, networks and dependability. His main interest lies in the fundamental principles that underly the design and the construction of distributed computing systems. He has been Principal Investigator of a number of research grants in these areas, and has been invited by many universities all over the world to give lectures on distributed algorithms and distributed computing. His h-index is 31. Professor Michel Raynal belongs to the editorial board of several international journals (including JPDC and IEEE TPDS). He has published more than 100 papers in journals, has served in program committees for more than 70 international conferences, chaired the program committee of more than 15 international conferences. Michel Raynal received the IEEE ICDCS best paper Award three times in a row: 1999, 2000 and 2001. He chairedthe steering committee leading the DISC symposium series in 2002-2004, and is a member of the steering committees of the following conferences: ACM PODC (ACM Symposium on the Principles of Distributed Computing), SIROCCO (Colloquium on Structural Information and Communication Complexity), and ICDCN (Int'l Conference on Distributed Computing and Networks).
Department of Computer Sciences - Colloquium
Speaker Name/Affiliation: Greg Hamerly/Baylor University
Friday, May 4, 2007, 10:00 a.m. - 11:00 a.m., ACES 6.304
Host: Inderjit Dhillon
"PG-means: learning the number of clusters in data"
Talk Abstract:
We present a novel algorithm called PG-means which is able to learn the number of clusters in a classical Gaussian mixture model. Our method is robust and efficient; it uses statistical hypothesis tests on one-dimensional projections of the data and model to determine if the examples are well represented by the model. In so doing, we are applying a statistical test for the entire model at once, not just on a per-cluster basis. We show that our method works well in difficult cases such as non-Gaussian data, overlapping clusters, eccentric clusters, high dimension, and many true clusters. Further, our new method provides a much more stable estimate of the number of clusters than existing methods. This was joint work with Yu Feng,
presented at NIPS 06.
Speaker Bio:
Greg Hamerly is an assistant professor of computer science at Baylor University. His research is in machine learning, particularly in unsupervised learning algorithms and their applications. He is a primary contributor to the SimPoint project, which uses unsupervised learning for efficient computer processor simulation.
UTCS Colloquium/AI
Nicholas Roy/Massachusetts Institute of Technology
Monday, April 30, 2007, 11:00 a.m, ACES 2.302
Host: Ben Kuipers
"Planning in Uncertain Worlds: Exploration and Information Gathering"
Talk Abstract:
Decision making in uncertain and incomplete models is an essential capability of robots operating in natural, dynamic domains. Separating model learning and planning into two distinct processes simplifies both problems, but prevents the planner from deliberately learning more to improve its own performance. In my group we have developed two approaches for planning in the information space of models; these algorithms allow a robot to generate plans that are robust to model errors while planning to learn more about the world. I will present results of our work in the domains of robot navigation and human-robot dialogue management.
Speaker Bio:
Nicholas Roy is the Boeing Assistant Professor in the Department of Aeronautics & Astronautics at the Massachusetts Institute of Technology. He received his Ph. D. in Robotics from Carnegie Mellon University, Pittsburgh in 2003. He is a member of the Computer Science and Artificial Intelligence Laboratory (CSAIL) at MIT. His research interests include autonomous systems, mobile robotics, human-computer interaction, decision-making under uncertainty and machine learning.
UTCS Colloquium/AI
Gregory Dudek/ McGill University
Friday, April 27, 2007 at 11:00a.m.
TAY 3.128 - East Wall (chalkboard)
Host: Peter Stone
"Vision-Based Behavior Control for Underwater Robotics"
Talk Abstract:
This talk discusses an ongoing research effort regarding the development of autonomous underwater vehicles, with particular emphasis on vision-based sensing. We have been developing an underwater vehicle for several applications, notably the environmental assessment of coral reefs habitats. Semi- autonomous behavior underwater is especially challenging since it combined 6 degree of freedom mobility, restricted communications, hard real-time constraints and unstructured environments. I will describe the system design of a small underwater and amphibious robot that uses computer vision as its principal sensing modality, and some of the ongoing challenges we have encountered. This includes an outline and discussion of how to accomplish operator control of the vehicle using a vision- based human-robot interface. The exploits a combination of a symbol-recognition system with a gestural inference and a special- purpose visual language. We also make use of Markov Random Fields for color correction (and, we hope, for scene reconstruction) I will comment on the use of physical feedback for behavior control and the development of a vision-based user interface. This
is join work with doctoral candidates Philippe Giguere and Junaed Sattar, as well as Anqi Xu and out colleagues at York University led by Michael Jenkin.
Speaker Bio:
Gregory Dudek is a Professor with the School of Computer Science, and an Associate member of the Department of Electrical Engineering at McGill University. He is the Director of McGill's Research Center for Intelligent Machines, a 20 year old inter-faculty research facility. In 2002 he was named a William Dawson Scholar (an honorary chair). He directs the McGill Mobile Robotics Laboratory.
He has recently been on the organizing and/or program committees of Robotics: Systems and Science, the IEEE International Conference on Robotics and Automation (ICRA), the IEEE/RSJ International Conference on Intelligent Robotics and Systems (IROS), the International Joint Conference on Artificial Intelligence (IJCAI), Computer and Robot Vision, IEEE International Conference on Mechatronics (ICM2005) and International Conference on Hands-on Intelligent Mechatronics and Automation (HIMA2005) among other bodies. He is president of CIPPRS, the Canadian Information Processing and Pattern Recognition Society,
an ICPR national affiliate.
He was on leave in 2000-2001 as Visiting Associate Professor at the Department of Computer Science at Stanford University and at Xerox Palo Alto Research Center (PARC). He obtained his PhD in computer science (computational vision) from the University of Toronto, his MSc in computer science (systems) at the University of Toronto and his BSc in computer science and physics at Queen's University.
He has published over 150 research papers on subjects including visual object description and recognition, robotic navigation and map construction, distributed system design and biological perception. This includes a book entitled "Computational Principles of Mobile Robotics" co-authored with Michael Jenkin and published by Cambridge University Press. He has chaired and been otherwise involved in numerous national and international conferences and professional activities concerned with Robotics, Machine Sensing and Computer Vision. He research interests include perception for mobile robotics, navigation and position estimation, environment and shape modelling, computational vision and collaborative filtering.
UTCS Colloquium/AI
Michael L. Littman/Rutgers University
Friday, April 20, 2007 11:00 - Noon - ACES 6.304
Host: Peter Stone
"Advancing the Theory and Practice of Model-based Reinforcement Learning"
Talk Abstract:
Reinforcement learners seek to minimize sample complexity, the amount of experience needed to achieve adequate behavior, and computational complexity, the amount of computation needed per experience. Focusing on these two issues, we have been developing theoretically motivated algorithms that exhibit practical advantages over existing learning algorithms. I will present some of my lab's more recent theoretical accomplishments as well as some video footage of robots learning.
Speaker Bio:
Michael L. Littman directs the Rutgers Laboratory for Real-Life Reinforcement Learning (RL3) and his research in machine learning examines algorithms for decision making under uncertainty. After earning his Ph.D. from Brown University in 1996, Littman worked as an assistant professor at Duke University, a member of technical staff in AT&T's AI Principles Research Department, and is now an associate professor of computer science at Rutgers. Both Duke and Rutgers awarded him teaching awards and his research has been recognized with three best-paper awards on the topics of computer crossword solving, complexity analysis of planning, and efficient reinforcement learning. He served on the executive council of the American Association for Artificial Intelligence, and is an advisory board member of the Journal of Artificial Intelligence Research and an action editor of the Journal of Machine Learning Research.
Speaking of Biology
Physiology & Behavior/Ecology, Evolution, & Behavior Dissertation Defense
Haruka Wada
"Stress and development: Ontogeny and cost/benefit of corticosterone secretion in an altricial bird."
Friday, April 20 - 12:00 p.m. - PHR 4.114
Host: Dr. David Crews
Speaking of Biology
Integrative Graduate Education and Research Traineeship Program
Denis Wirtz, Ph.D.
Professor, Department of Chemical & Biomolecular Engineering & Institute for NanoBio Technology, Johns Hopkins University
"Cell Microrheology in Health and Disease."
Friday, April 20 - 1:00 p.m. - ACE 2.402
Host: Muhammad Zaman
Speaking of Biology
Cognition and Perception
Bas Rokers
Imaging Research Center & Center for Perceptual Systems, UT-Austin
"Neural computation of motion through depth is robust to binocular anticorrelation."
Friday, April 20 - 3:00 p.m. - SEA 3.250
Speaking of Biology
Texas Neuroscience Review Mini-Symposium and Debut
Dr. Michael Domjan
The Imaging Research Center, UT-Austin
"Magnetic Resonance Imaging: A new methodology for the neurosciences."
&
Dr. Alex Huk
Section of Neurobiology, UT-Austin
"Neural basis of human perception and cognition: insights from neuroimaging."
3:00 p.m. - PHR 2.108
Host: Texas Neuroscience Review
A reception will be held in conjunction with the College of Natural Sciences Undergraduate Research Forum following the seminar, where the publication of the first issue of Texas Neuroscience Review will be announced.
Speaking of Biology
Section of Integrative Biology
Dr. Sam Sweet
"Comparative spatial ecology of small varanid lizards in northern Australia."
Thursday, April 19 - 2:00 p.m. - PHR 4.114
Host: Dr. Eric Pianka
Speaking of Biology
2007 Annual Burdette Lecture
Steven McKnight, Ph.D.
Professor, University of Texas Southwestern Medical School at Dallas
"Title TBA."
Thursday, April 19 - 2:30 p.m. - Texas Union Theatre
Speaking of Biology
Biomedical Engineering
Dr. Edward H. Shortliffe
Dean of the Faculty, University of Arizona College of Medicine, Phoenix
"Biomedical Informatics: Defining the Science and Enhancing Decisions."
Thursday, April 19 - 3:30 p.m. - ACE 2.302
Speaking of Biology
Section of Molecular Genetics and Microbiology
Susan Rosenberg, Ph.D.
Cullen Professor of Molecular Genetics, Baylor College of Medicine, Houston, TX
"Genome Instability, Spontaneous DNA Breakage, and Regulation of Evolvability."
Wednesday, April 18 - 4:00 p.m. - ESB 223
Host: Makkuni Jayaram
Department of Computer Sciences - Colloquium
Jay Wylie/HP Labs
Wednesday, April 18, 2007 at 2:00p.m. - ACES 6.304
Host: Lorenzo Alvisi
"Determining fault tolerance of XOR-based erasure codes efficiently"
Talk Abstract:
XOR-based erasure codes have had a tremendous impact on networked systems in the recent past. For example, LDPC codes, digital fountain codes, and rateless erasure codes have all been deployed in P2P systems and streaming multicast systems. The impact of such codes on clustered storage systems has not yet been felt. Replication and RAID continue to dominate clustered storage systems. We believe that a clear understanding of XOR-based erasure codes applicable to clustered storage systems, rather than networked systems, will facilitate their adoption in clustered storage systems.
Towards this end, we propose a new fault tolerance metric for XOR-based erasure codes: the minimal erasures list (MEL). A minimal erasure is a set of erasures that leads to irrecoverable data loss and in which every erasure is necessary and sufficient for this to be so. The MEL is the enumeration of all minimal erasures. The MEL completely describes the fault tolerance of an XOR-based erasure code at and beyond its Hamming distance; it is therefore a useful metric for comparing the fault tolerance of such codes. We also propose an algorithm that efficiently determines the MEL of an erasure code. We use the proposed algorithm to identify the most fault tolerant XOR-based erasure code for all possible systematic erasure codes with up to seven data symbols and up to seven parity symbols. These codes are directly applicable in clustered storage systems today.
Speaker Bio:
Jay J. Wylie is a Research Scientist in the Storage Systems Department at Hewlett-Packard Labs. He received his Ph.D. and M.S. degrees in Computer Engineering from Carnegie Mellon University in 2005 and 2000 respectively. He received his B.A.Sc. in Systems Design Engineering from the University of Waterloo in 1998. Jay's interests are distributed systems, storage systems, erasure codes, (Byzantine) fault-tolerance, and dependability. Jay can be reached by email at jay.wylie@hp.com
Department of Computer Sciences/Center for Computational Biology & Bioinformatics - Colloquium
There is a sign up schedule for this event: http://www.cs.utexas.edu/department/webevent/utcs/events/cgi/list_events.cgi
Alexandros Stamatakis
Ecole Polytechnique Federale de Lausanne School of Comp & Communication Sciences
Tuesday, April 17, 2007, 2:00 p.m. - 3:30 p.m., TAY 3.128 (East Wall)
Host: Tandy Warnow
"Faster Algorithms for Support Value Computation & Emerging Parallel Architectures for Phylogeny Reconstruction"
Talk Abstract:
Despite the impressive progress that has been achieved with the new generation of Maximum Likelihood (ML) search algorithms, the computation of support values based on non-parametric bootstrapping (BS) still represents a major computational challenge.
Initially, I will discuss why the Randomized Estimated Log Likelihood (RELL) method is probably very hard to apply to large real-world datasets. Thereafter, I will present new heuristics to accelerate the BS procedure in RAxML (Randomized Axelerated Maximum Likelihood). In comparison to the standard BS procedure these heuristics yield run time improvements between factor 7 on datasets with 500 sequences up to factor 14 on 1,700 sequences. At the same time the support values obtained by the new BS heuristics show correlation coefficients ranging between 0.94 and 0.96 compared to those obtained via the standard method. In absolute numbers this means that 100 bootstrap replicates on single-gene datasets up to 2,000 taxa can be conducted within less than 24 hours on a single - reasonably fast - processor.
In the second part of my talk I will outline how the computation of large multi-gene datasets with ML can efficiently be parallelized on hardware platforms with very distinct architectures such as the IBM Cell and the IBM BlueGene. The parallelization on BlueGene scales well up to 512 processors on the largest dataset analyzed under ML to date, which consists of 270 sequences and 500,000 base pairs.
I will conclude with an overview of current work on related projects.
Related papers (PDF) and software (open source code for Mac/Linux) available at: icwww.epfl.ch/~stamata
Department of Computer Sciences - Faculty Candidate
Kristen LeFevre, University of Wisconsin-Madison
April 17, 2007 - 11:00 a.m. - ACES 2.302
Host: Don Batory
"Anonymization Techniques for Published Data"
Many organizations publish and distribute non-aggregate personal data for purposes including medical, demographic, and public health research. For legal and ethical reasons, it is important that these organizations take steps to protect the identities of individuals, as well as their sensitive personal information. At the same time, concern for privacy must be balanced with the need to provide useful, high-quality data.
In this talk, I will first give a brief overview of the anonymity problem in data publishing. Then I will describe a new multidimensional generalization approach (also commonly called "recoding") and greedy algorithmic framework.
The contributions of this work span two key dimensions: First, there are a seemingly infinite number of ways to measure data quality. I will take a very direct evaluation approach, based on a target workload of queries and data mining tasks, and I will describe some ways to directly incorporate knowledge of a workload into the anonymization process. Second, as more and more personal information is collected, it is important to develop algorithms that are both efficient and scalable. In the latter part of the talk, I will describe techniques for incorporating scalability into our algorithmic framework.
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-DNA Repair Group Series
Dr. Masaaki Moriya
SUNY, Stonybrook, NY
"DNA repair and mutagenesis of ROS-generated lesions."
Tuesday, April 17 - 11:30 a.m. - Videoconferenced to Harrison Auditorium, Pickle Conference
Center, Science Park, Smithville, TX
For directions to the Science Park, go to: http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Biochemistry Division Seminar
David E. Draper, Ph.D.
Vernon E. Krieble Professor of Chemistry, Johns Hopkins University
"Getting the Charge Out of RNA: How Ions Help RNA Fold."
Tuesday, April 17 - 2:00 p.m. - MBB 1.210 - Refreshments will be served at 1:45 p.m.
Hosts: Robin Gutell, Ph.D. & Rick Russell, Ph.D.
Speaking of Biology
Department of Computer Sciences
Alexandros Stamatakis
School of Comp & Communication Sciences, Ecole Polytechnique Federale de Lausanne
"Faster Algorithms for Support Value Computation & Emerging Parallel
Architectures for Phylogeny Reconstruction."
Tuesday, April 17 - 2:00 p.m. - TAY 3.128
Host: Tandy Warnow
There is a sign up schedule for this event at
http://www.cs.utexas.edu/department/webevent/utcs/events/cgi/list_events.cgi
Speaking of Biology
Section of Molecular Cell and Developmental Biology
Dr. David Stein
Section of Molecular Cell and Developmental Biology, UT-Austin
"The Drosophila Embryonic Dorsal-Ventral Axis - Naturally Sweetened, with a Hint of Sulfate."
Tuesday, April 17 - 4:00 p.m. - MBB 1.210 - Refreshments will be served at 3:30.
Speaking of Biology
Population Biology
Samraat Pawar
Section of Integrative Biology, UT-Austin
"Webs in an ever-changing world: environmental fluctuations and population interaction networks."
Monday, April 16 - 12:00 p.m. - MBB 1.210
Speaking of Biology
Center for Perceptual Systems
Emo Todorov, Ph.D.
Assistant Professor, Department of Cognitive Science, University of California San Diego
"Optimality of Activity Sensing."
Reception with Refreshments at 11:30 AM
Monday, April 16 - 12:00 p.m. - SEA 4.244 - Reception with refreshments at 11:30 a.m.
Host: Dana H. Ballard
Speaking of Biology
Section of Neurobiology
Catharine Rankin, Ph.D.
University of British Columbia
"A Genetic Dissection of Memory in C. elegans."
Monday, April 16 - 4:00 p.m. - MBB 1.210
Host: Dr. Harold Zakon
Speaking of Biology
UT Anthropological Society
Dr. Thad Q. Bartlett
Assistant Professor, Department of Anthropology, UT-San Antonio
"The Sex Life of Andromeda: A Case Study in So-Called Gibbon Monogamy."
Monday, April 16 - 5:00 p.m. - EPS 1.128
Speaking of Biology
Section of Neurobiology Recruitment Seminar
Nicholas Priebe, Ph.D.
University of California, San Francisco
"Chalk Talk."
Friday, April 13 - 12:00 p.m. - NMS 1.120
Speaking of Biology
Physiology & Behavior
Dr. Sergey Nuzhdin
University of California-Davis
"Flies Socializing: Contributions To The Maintenance Of Genetic Variation In Behaviors."
Friday, April 13 - 12:00 p.m. - PHR 4.114
Host: Dr. David Crews
Speaking of Biology
Integrative Graduate Education and Research Traineeship Program
Carolyn Bayer, IGERT Trainee, Department of Biomedical Engineering
"Synthesis and Characterization of a Hydrogel-Conductive Polymer Composite."
Advisors: Nicholas Peppas and Lynn Loo
&
Eric Spivey, IGERT Trainee, Department of Biomedical Engineering
"Functionalization of Multi-Photon Crosslinked Protein Microstructures."
Advisors: Jason Shear and Andy Dunn
Friday, April 13 - 1:00 p.m. - ACE 2.402
Speaking of Biology
Biochemistry Division Seminar
Christopher K. Mathews, Ph.D.
Professor Emeritus, Biochemistry & Biophysics Department, Oregon State University
"Maintaining Precursor Pools for Mitochondrial DNA Replication."
Friday, April 13 - 1:30 p.m. - WEL 2.122
Host: Dean R. Appling, Ph.D
Speaking of Biology
Section of Molecular Genetics and Microbiology
Dr. David Johnson
UT M.D. Anderson Cancer Center, Smithville, TX & Adjunct Assoc. Prof.,
Section of Molec. Genetics & Microbiology, UT-Austin
"Research in Progress."
Friday, April 13 0 3:30 p.m. - MBB 1.210
Host: Liz Wyckoff
Department of Computer Sciences - Faculty Candidate
Edmund Nightingale, University of Michigan
April 12, 2007 - 11:00a.m. - ACES 2.302
Host: Emmett Witchel
"Improving the Performance of Highly Reliable Software Systems"
Commodity operating systems still retain the design principles developed when processor cycles were scarce and RAM was precious. These out-dated principles have led to performance/functionality trade-offs that are no longer needed or required; I have found that, far from impeding performance, features such as safety, consistency and energy-efficiency can often be added while improving performance over existing systems.
I will describe my work developing Speculator, which provides facilities within the operating system kernel to track and propagate causal dependencies. Using Speculator, I will show that distributed and local file systems can provide strong consistency and safety guarantees without the poor performance these guarantees usually entail.
Speaking of Biology
Section of Integrative Biology
Dr. Sergey Nuzhdin
University of California-Davis
"Genetic variation and evolution of transcriptional networks."
Thursday, April 12 - 2:00 p.m. - MBB 1.210
Host: Dr. Johann Hofmann
Speaking of Biology
Section of Neurobiology Recruitment Seminar
Nicholas Priebe, Ph.D.
University of California, San Francisco
"The role of local circuitry and spike threshold in cortical processing."
Thursday, April 12 - 4:00 p.m. - ACES 2.402
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-Hogg Seminar Series
Leland Chung, Ph.D.
Emory University School of Medicine, Atlanta, GA
"The surprising role of a house keeping gene, beta 2 microglobulin, in cancer growth and metastasis."
Wednesday, April 11 - 11:00 a.m. - Harrison Auditorium, Pickle Conference Center, Science
Park, Smithville, TX
For directions to the Science Park, go to: http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Section of Molecular Genetics and Microbiology
Jimmy Ballard, PhD
Associate Professor, University of Oklahoma Health Sciences Center, Oklahoma City, OK
"Elucidating the Cardiotoxic Activity of Clostridium difficile Toxin B."
Wednesday, April 11 - 4:00 p.m. - ESB 223
Speaking of Biology
Marine Science Institute-Schweppe Speaker
Dr. Graham Young
University of Washington
"Environmental and endocrine regulation of the ovary: salmonid and freshwater eel models."
Tuesday, April 10 - 3:45 p.m. - Visitors Center Auditorium at the Marine Science Institute,
Port Aransas, TX
For directions to the Marine Science Institute, go to: http://msi40.utmsi.utexas.edu/institute/maps.htm
Speaking of Biology
Section of Molecular Cell and Developmental Biology
Dr. Sarah Hake
Department of Plant & Microbial Biology, University of California, Berkeley
"MicroRNA Regulation of Inflorescence Development in Maize."
Tuesday, April 10 - 4:00 p.m. - MBB 1.210 - Refreshments will be served at 3:30.
Host: Enamel Huq
Department of Computer Sciences - Faculty Candidate
Adrien Treuille, University of Washington
Tuesday, April 10, 2007, 11:00 a.m. - Noon - ACES 2.302
Host: Okan Arikan
"New Approaches to Modeling and Control of Complex Dynamics"
Talk Abstract:Complex phenomena such as animal morphology, human motion, and large fluid systems challenge even our most sophisticated simulation and control techniques. My overarching research goal has been to develop fundamentally new methods to approach such high-dimensional and nonlinear problems. This talk presents my work solving these problems across a wide range of phenomena, including a new model-reduction approach to fluids that is orders-of-magnitude faster than standard simulation methods and enables interactive high-resolution fluid simulation for the first time. Another example is a continuum approach to crowd dynamics which efficiently reproduces empirical aspects of large crowd behavior that would be difficult or impossible to achieve with traditional agent models. The talk will also cover work on several other phenomena including human animation, and protein folding. Such new algorithmic approaches advance
not only our ability to simulate and control complex systems but also our understanding of the systems themselves.
Speaking of Biology
Population Biology
Rob Plowes
Section of Integrative Biology, UT-Austin
"Invasives at Their Limit: Fire Ants in Texas."
Monday, April 9 - 12:00 p.m. - MBB 1.210
Host: Dr. Larry Gilbert
Center for Perceptual Systems
Robert Jacobs, Ph.D.
Department of Brain and Cognitive Sciences, University of Rochester
"Near-Optimal Decision-Making in Dynamic Environments."
Monday, April 9 - 12:00 p.m. - SEA 4.244 - Reception with refreshments at 11:30 a.m.
Speaking of Biology
Center for Nonlinear Dynamics
Dr. Richard Aldrich
Chair, Section of Neurobiology, UT-Austin
"Biophysics of ion channels - the molecular units of bioelectric signaling."
Monday, April 9 - 1:00 p.m. - RLM 11.204
Speaking of Biology
Plant Biology Graduate Program
Dr. Rowan Sage
University of Toronto
"The Evolution of C4 Photosynthesis."
Monday, April 9 - 4:00 p.m. - BUR 136 - Refreshments will be served at 3:30 p.m. in BIO 214 before the seminar.
Host: Debra Hansen
Speaking of Biology
Section of Neurobiology
Mary Kennedy, Ph.D.
California Institute of Technology
"A new look at mechanisms of synaptic plasticity."
Monday, April 9 - 4:00 p.m. - MBB 1.210
Host: Dr. Kristen Harris
Department of Computer Sciences - Faculty Candidate
Speaker Name: Lek-Heng Lim, Stanford University
April 5, 2007, 11:00 a.m., ACES 2.302
Host: Inderjit Dhillon
"Ten Ways to Decompose a Tensor and Their Applications in Data Mining"
Talk Abstract:
In scientific and statistical computing, one often reduces the problem at hand -- be it a problem involving differential equations or nonlinear optimization or parameter estimation-- to a simpler problem (or a sequence of these) that requiresnothing more than linear algebra. In fact, the solution of linear systems alone accounts for more than 70% of all supercomputing time in the world.
However, with the use of increasingly sophisticated sensor devices, experimental methodologies, and mathematical models, we now see a new generation of problems in scientific and statistical computing that cannot be reduced to standard problems in numerical linear algebra. It is thus pertinent to enlarge the arsenal of computational tools available at our disposal. Among the various plausible extensions to numerical linear algebra, one will find the capability of dealing with multilinearity to be among the most natural, desirable, and powerful -- if we could do tensor computations (numerical multilinear algebra) as effectively as matrix computations (numerical linear algebra), then we would be able to address many of the new problems arising in modern scientific and statistical computing.
It is not coincidental that "the decompositional approach to matrix computations" has been named one of the Top 10 Algorithms of the 20th Century. If numerical linear algebra is the foundation of scientific computing, then matrix decompositions may be considered to be the foundation of numerical linear algebra. So the development of numerical multilinear algebra ought to begin with a few basic tensor decompositions.
In this talk, we will present ten decompositions of tensors and discuss their properties and applications. Our list will include the tensorial generalizations of LU/LDU decomposition, QR/complete orthogonal factorization, eigenvalue decomposition (EVD), singular value decomposition (SVD), nonnegative matrix factorization (NMF), Kronecker product decomposition, and more. We will discuss the similarities and differences of these decompositions with their matrix counterparts, as well as the various challenges in numerical multilinear algebra, of which these tensor decompositions form a cornerstone.
To every tensor decomposition, there is an associated approximation problem. We will see how these may be applied to multilinear statistical models that generalize vector space models, independent component analysis, graphical models/Bayesian networks, and model reduction. We will illustrate these with selected applications in bioinformatics, computer vision, signal processing, spectroscopy, and sensor locations.
Department of Biomedical Engineering Seminar Series 2006-2007
C. Mauli Agrawal, Ph.D.
Dean, College of Engineering, Professor and Director, Institute for Bioengineering and Translational Research, Peter Flawn Professor The University of Texas at San Antonio
April 5, 2007 - 3:30 p.m. - ACE 2.302
"Surface Modification of Biomaterials for Cardiovascular Applications"
Different strategies related to surface modification of biomaterials for cardiovascular applications will be discussed. This will include the use of gas-plasma treatment of polymeric materials to elicit angiogenesis in tissue engineering applications. Our studies show that gas-plasma treatment of polylactic acid induces endothelial cells to up-regulate VEG-F production. This knowledge is being used to designed scaffolds for regenerating vascularized tissue. In a separate part of the talk the use of self-assembled monolayers for drug-delivery applications will be presented. This approach has implications for drug-eluting cardiovascular stents as well as for orthopedic and dental implants.
Support for the seminar series is provided by our Industrial Affiliates.
Department of Biomedical Engineering
http://www.bme.utexas.edu
The Austin Forum (www.austinforum.org)
When: Wednesday, April 4, 2007 @ 6:30 p.m.
Where: J.J. Pickle Research Campus-Research Office Complex (Jackson School of Geosciences & Texas Advanced Computing Center's new building), Seminar Room 1.603
The Texas Advanced Computer Center (TACC) and The Austin Forum invite you to a participatory talk by Dr. Charles Jackson, a leading research scientist at The University of Texas at Austin's Institute for Geophysics (UTIG). Dr. Jackson will present some of the little-known inner-workings of climate model development, including what can and cannot be predicted about the Earth's future climate. Are predictions of future global warming and its consequences accurate?
The mission of The Austin Forum is to promote awareness of issues and opportunities in our community and to enrich lives. The Forum invites distinguished professionals and leaders to speak on topics related to science and technology and how they impact society.
Learn more about The Austin Forum's upcoming events at: www.austinforum.org
**This event is free and open to the public; complimentary food and drink will be provided prior to the talk @ 6:00 p.m.
For more detailed information, please contact:
Rebeka Villarreal Martinez
Development & External Relations
Texas Advanced Computing Center
Direct: 512-232-7794
Fax: 512-475-944
Scientific Software Day
Where:
The University of Texas at Austin
J.J. Pickle Research Campus, Research Office Complex (ROC, Bldg. 196)
Seminar Room (Room 1.603), 10100 Burnet Road, Austin, TX 78758
When:
Monday, April 2, 2007 - 9:00am - 4:00pm (CDT)
The Bureau of Economic Geology (BEG) and the Texas Advanced Computing Center (TACC) invite you to participate in Scientific Software Day - a day designed to provide practical introductions to several software packages relevant to the research and science communities.
Speakers from the University and Austin area companies will showcase software (mostly open-source) that is of general use to scientific researchers. Presentations covering several topics are planned, including:
* linear algebra software (Petsc, Flame);
* workflow (Madagascar, MyCluster); and
* programming languages and environments (Eclipse, DataRush, LabView, Scientific Python, GridChem).
There are two slots available for additional talks. If you would like to participate as a presenter, send email, by Monday, March 19th, to softwareday@tacc.utexas.edu. Requests will be reviewed and selections made by the event organizers.
Attendance is free, but registration is required. Please register at http://www.tacc.utexas.edu/softwareday/.
Email any questions you may have to softwareday@tacc.utexas.edu.
Organizers:
Victor Eijkhout
Texas Advanced Computing Center
Phone: 512.471.5809
Sergey Fomel
Bureau of Economic Geology
Phone: 512.475.9573
Please see the following URL for directions to Pickle Research Campus and the Research Office Complex: http://www.tacc.utexas.edu/general/visitor/.
Victor Eijkhout,
512 471 5809 (w)
Texas Advanced Computing Center,
The University of Texas at Austin
UTCS Colloquia
Brent Waters, SRI International
Monday, April 2, 2007, 11:00a.m. - 12:00p.m., ACES 6.304
Host: Vitaly Shmatikov
"Attribute-Based Encryption: A Cryptosystem for Expressive Access Control on Encrypted Data"
Talk Abstract:
Several distributed file and information systems require complex access-control mechanisms, where access decisions depend upon attributes of the protected data and access policies assigned to users. Traditionally, such access-control mechanisms have been enforced by a server that acts as a trusted reference monitor; the monitor will only allow a user to view data if his access policy allows it. While the use of trusted servers allows for a relatively straightforward solution, there is a large downside to this approach --- both the servers and their storage must be trusted and remain uncompromised. A natural solution to this problem is to encrypt stored data. However, traditional public-key encryption methods require that data be encrypted to one particular user's public key and are unsuitable for expressing more complex access control policies.
In this talk, I will present recent work on a new cryptographic primitive, called Attribute-Based Encryption (ABE), that was created to address this issue. Attribute-Based Encryption allows for expressive access policies over encrypted data. In an ABE system encrypted data is annotated with descriptive attributes and users' private keys are ascribed access formulas over these attributes. For example, if Carol is assigned to read and process systems-seminar messages during the year 2007, she would be ascribed the private key with the access formula "Subj:Systems-Seminar" AND "Year:2007".
I will focus this talk on the challenges of creating ABE systems that are both secure and efficient. In particular, an ABE system must be secure against an attacker that collects several private keys from different colluding users. We also want to avoid designs that are prohibitively expensive; for example, a solution should not include a separate public key/private for every possible access control policy that might ever be used. In addition, I will talk about recent efforts in implementing Attribute-Based Encryption and making it available as a tool to be used by researchers in systems security.
UTCS Colloquium - Artificial Intelligence
Renata Vieira, UNISINOS, Sao Leopoldo, Brazil
Friday, March 30, 2007 2:00 p.m. - ACES 2.402
Host: Raymond Mooney
"Have I mentioned it?"
Talk Abstract:
Coreference resolution is a well known NLP task, relevant for the more general task of information extraction, among others. A related problem is the problem of identifying if a referring expression is introducing a new entity in the text or if it follows previously mentioned ones. Definite descriptions are a type of referring expressions which are highly ambiguous between these two roles. In fact they sometimes lie in between these two, when mentioning a new entity whose interpretation is anchored in given ones. When developing a classifier that distinguishes between these many roles of definite descriptions we face not only the old AI problem of grasping common sense and world knowledge but also the problem of unbalanced data. In this talk I will present some experiments dealing with these problems and I will mention some NLP tasks that the classifier is useful for.
Speaker Bio:
Renata Vieira is Professor in the Computer Science Department at Universidade do Vale do Rio dos Sinos, Sao Leopoldo, Brazil. She received her PhD from the University of Edinburgh in 1998. Her research interests cover issues in computational linguistics, artificial intelligence, including natural language understanding, discourse processing, agent communication, knowledge representation, ontologies and the semantic web.
UTCS Colloquium/ICES/CS Seminar
Anthony R. Ingraffea, Cornell University
March 30, 2007, 11:00a.m. - 12:00p.m., ACE 6.304
Host: Keshav Pingali
"Multi-Scale Computational Simulation of Fatigue Cracking Processes in Aluminum Alloys"
Talk Abstract:
We are developing physics-based models for simulating nucleation and propagation of fatigue cracks in aluminum alloys. Our models are part of a DARPA-funded, broad-team project on structural integrity prognosis. The salient features of our approach are:
A. The use of statistically representative, realistic microstructures as a starting point for our simulations. Using unique microstructure builder tools, we assemble three-dimensional digital material representations from actual microstructural observations. These contain realistic morphologies, textures, particle distributions, etc. Constituents are assigned statistically representative distributions of properties such as yield strengths and toughnesses.
B. The use of polycrystal plasticity models to accurately compute stress and strain fields in polycrystals using the finite element method. In polycrystalline metals, the grain structure and phenomena occurring on the grain scale, such as interactions between grains and particles and crystallographic slip, strongly influence the fatigue behavior of the materials. Statistically realistic 3D microstructures are directly simulated in order to investigate the effect of elasto-plastic response within the microstructure on the fatigue behavior.
C. The use of an explicit geometric representational approach in a multi-scale methodology. At each length scale, fatigue crack precursors, such as grain boundary or particle decohesion, are represented geometrically in the finite element model, and allowed to evolve through changes in the underlying geometric and mesh models. The need for concomitant quantitative experimental data on microstructural damage nucleation (particle fracture, debonding, etc) becomes apparent.
I will report on progress in development, verification, and validation of our simulation models, and show example simulations
UTCS Colloquium/ICES/CS Seminar
Johannes Gehrke, Cornell University
March 30, 2007, 10:00a.m. - 11:00a.m., ACES 2.402
Host: Keshav Pingali
"Scaling Computer Games to Epic Proportions"
Talk Abstract:
An important aspect of computer games is the artificial intelligence (AI) of non-player characters. To create interesting AI in games today, developers and players can either create complex, dynamic behavior for a very small number of characters, or they can create simple behavior for a large number of characters, but neither the game engines nor the style of AI programming permits complex behavior that scales to a very large number of non-player characters.
I will show how we can take techniques that currently enable database systems to scale to petabytes and apply them to scale computer games and simulations. I will describe a highly expressive scripting language SGL (for Scalable Gaming Language) for customizing behavior for individual non-player characters. The use of sophisticated query processing and indexing techniques allows us to efficiently execute a large number of SGL scripts, thus providing a framework for games with a truly epic number of non-player characters. I will conclude with an outlook how our techniques can be used to also achieve significant scalability in large-scale simulations.
This talk describes joint work with Alan Demers (Cornell), Christoph Koch (Saarland University), Rajmohan Rajagopalan (Cornell), and Walker White (Cornell).
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-Departmental Seminar Series
Linda Hendershot, Ph.D.
St. Jude Children's Research Hospital, Memphis, TN
"The unfolded protein response in tumor cells and the effects on chemosensitivity."
Friday, March 30 - 11:00 a.m. - Harrison Auditorium, Pickle Conference Center, Science
Park, Smithville, TX
For directions to the Science Park, go to: http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Ecolunch
Krushnamegh Kunte
Ecology, Evolution, & Behavior Graduate Program
"Removal of dominant species increases diversity in nectar-feeding butterfly communities."
Friday, March 30 - 12:00 p.m. - BIO 214
Speaking of Biology
McCraw Kinesiology Departmental Lecture Series
Lisa Griffin, Ph.D.
Department of Kinesiology and Health Education, UT-Austin
"Neural Adaptations to Fatigue and Training: Applications to Spinal Cord Injury Rehabilitation."
Friday, March 30 - 12:00 p.m. - BEL 962 - Refreshments will be provided at 11:45.
Speaking of Biology
Physiology & Behavior
David Haig
Department of Organismic and Evolutionary Biology, Harvard University
"Prader-Willi syndrome and the evolution of human childhood."
Friday, March 30 - 12:00 p.m. - PHR 4.114
Host: Dr. David Crews
Speaking of Biology
Biochemistry Division Seminar
Lizbeth Hedstrom, Ph.D.
Markey Professor of Biochemistry and Chemistry, Brandeis University
"IMP Dehydrogenase and the dynamics of drug selectivity."
Friday, March 30 - 1:30 p.m. - WEL 2.122
Host: Kevin N. Dalby, Ph.D.
Speaking of Biology
Cognition and Perception
Swathi Kiran
Department of Communication Sciences & Disorders
"The role of exemplar typicality within categories on recovery from brain damage."
Friday, March 30 - 3:00 p.m. - SEA 3.250
UTCS Colloquium/ACT Special Seminar
Anna Lysyanskaya/Brown University
Friday, March 30, 2007 - 11:00 a.m. - ACES 3.408
Host: Adam Klivans
"Compact Ecash and Applications"
Talk Abstract:
The main idea of electronic cash is that, even though the same party (a Bank) is responsible for giving out electronic coins, and for later accepting them for deposit, the withdrawal and the spending protocols are designed in such a way that it is impossible to identify when a particular coin was spent. I.e., the withdrawal
protocol does not reveal any information to the Bank that would later enable it to trace how a coin was spent. Since a coin is represented by data, and it is easy to duplicate data, an electronic cash scheme requires a mechanism that prevents a user from spending the same coin twice (double-spending), for example by identifying double-spenders and tracing all transactions that they have carried out.
In this talk, I will first present a scheme that allows a user to withdraw a wallet with W coins, such that the space required to store these coins, and the complexity of the withdrawal protocol, are proportional to logW, rather than to W. We achieve this without compromising the anonymity and unlinkability properties usually required of electronic cash schemes. We give a scheme that allows us to efficiently trace all coins that were spent by a double-spender. The security of our construction relies on a mix of cryptographic assumptions about groups with bilinear maps, and is in the random oracle model.
I will then show how to use the same methodology to achieve balance between accountability and privacy in other applications. In particular, we consider a setting where the amount of anonymous transactions with a particular merchant may be limited (e.g., so as to prevent money laundering). Finally, I will show that this methodology solves the problem of uncloneable group identification.
Based on joint papers with Jan Camenisch, Susan Hohenberger, Markulf Kohlweiss, and Mira Meyerovich.
Department of Computer Sciences - Faculty Candidate
Hovav Shacham, Weizmann Institute of Science
Thursday, March 29, 2007 11:00 a.m. - Noon - ACES 2.302
Host: Vitaly Shmatikov
"Buffer Overflows and Group Signatures: Recent Results in Security and Cryptography"
Talk Abstract:
We analyze the effectiveness of two techniques intended to make it harder for attackers to exploit vulnerable programs: W-xor-X and ASLR. W-xor-X marks all writable locations in a process' address space nonexecutable. ASLR randomizes the locations of the stack, heap, and executable code in an address space. Intel recently added hardware to its processors (the "XD bit") to ease W-xor-X implementation. Microsoft Windows Vista ships with W-xor-X and ASLR. Linux (via the PaX project) and OpenBSD also include support for both.
We find that both measures are less effective than previously thought, on the x86 at least. A new way of organizing exploits allows the attacker to perform arbitrary computation using only code already present in the attacked process' address space, so code injection is unnecessary. Exploits organized in the new way chain together dozens of short instruction sequences, each just two or three instructions long. Because of the properties of the x86 instruction set, these sequences might not have been intentionally compiled into the binary; we find them by means of static analysis. Furthermore, the effective entropy of PaX ASLR can be searched by brute force. The attack takes just a few minutes to mount over the network.
Group signatures are a variant of digital signatures that provides anonymity for signers. Any member of a group can sign messages, but the resulting signature keeps the identity of the signer secret. In some systems there is a third party that can undo the signature anonymity (trace) using a special trapdoor. New applications for group signatures include the trusted computing initiative (TCPA) and vehicle safety ad-hoc networks (DSRC). In each case, group signatures provide privacy guarantees for tamper-resistant embedded devices.
We describe a short group signature scheme. Signatures in our scheme are approximately the size of a standard RSA signature with the same security. The mathematical setting for our scheme is certain elliptic curves featuring an efficiently computable bilinear map, a setting that has proved fruitful in recent years. We also consider two choices for handling revocation in our scheme.
School of Biological Sciences - Distinguisted Lecturer
Dr. David Haig, Lorene Morrow Kelly Distinguished Lecturer
March 29 in ACES 2.302, 4:00pm, with a reception to follow.
To ask to be present at dinner on either evening, please contact the host, Mike Ryan, at mryan@mail.utexas.edu or 471-5078.
Below is some background on Dr. Haig:
David Haig, is an Australian evolutionary biologist and geneticist, associate professor in Harvard Department of Organismic and Evolutionary Biology. He is interested in intragenomic conflict, genomic imprinting and parent-offspring conflict, and wrote the book Genomic Imprinting and Kinship.
David Haig, Professor of Biology, Botanical Museum 42B
phone: (617) 496 5125, fax: (617) 495 5667, dhaig@oeb.harvard.edu
HARVARD GAZETTE ARCHIVES
Genes in conflict:
David Haig looks at internal genetic warfare
By William J. Cromie, Gazette Staff
Most people think of genes as molecules that make you more or less fit for survival. In healthy people, genomes are seen as well-functioning machines where all the parts work together for a common good.
That's not necessarily so, believes David Haig, a newly tenured professor in the Department of Organismic and Evolutionary Biology. "I'm interested in situations where genes in an individual have different fitnesses and can come into conflict with each other," he says.
He's not talking about genes with different functions battling for a top spot in your genome, but identical genes with different "attitudes."
All genes except those that determine sex come in pairs, one inherited from your mother and one from your father. In most cases, the result of such pairing never changes, there is no conflict. If you receive a gene for blue eyes from your mom and one for brown eyes from your dad, you wind up with brown eyes. If you inherit a gene for blue eyes from your dad and one for brown eyes from your mom, you still wind up with brown eyes.
But in genes that interest Haig, parental origin makes a difference. The gene does one thing if it comes in an egg cell and another if it comes in a sperm cell. What maximizes the fitness of the one is different from what maximizes the fitness of the other.
Haig cites the example of pregnancy. Nutrients are transferred to the fetus through the placenta, and the more food it receives, the healthier the baby will be. But that comes with a cost to the mother. The more nutrients she supplies, the less energy she has to devote to other offspring, and the more vulnerable she becomes to disease. Therefore, the genes that a fetus receives from its mother are most interested in mom's survival and reproduction in the future.
Genes from the father, however, take a different view. They demand the most from the mother during a pregnancy and are less interested in her future reproduction. There's even evidence that paternal genes are particularly active in the growth of the placenta, which would increase the amount of nourishment the fetus receives but increase the cost to the maternal genes. Therein lies the conflict.
Born to be a biologist
Naomi Pierce, Hessel Professor of Biology and Curator of Lepidoptera, remembers the first time she met Haig. "I was struck by his remarkable combination of unreserved affability and academic brilliance," she says. "He can explain phenomena ranging from crocodilian sex determination to genomic imprinting in the most lucid and engaging manner. He is particularly well known for his evolutionary explication of the latter - situations where a gene has a different pattern of expression depending on whether it is inherited from an individual's mother or father. His work has been important in explaining how this can lead to unusual aspects of mammalian development, including a number of human diseases."
These diseases include various forms of childhood cancer and a rare malady that produces dramatic overgrowth of a fetus. Many of these genes are involved in cell growth, and cancers are, basically, the uncontrolled growth and progression of cells.
Although born to be a biologist, Haig, now 44, didn't start out to work on such theoretical questions. His first interests were birds and plants. He was born in Canberra, the busy capital of Australia, which was more like a quiet country town then. Flocks of parrots used to fly in to drink at the family fishpond, and that got him interested in bird watching at the age of 7. His mother taught high school biology, and she added fuel to his interest in birds and plants.
Haig did undergraduate work at Macquarie University in Sydney, and entered graduate school with the idea of getting a Ph.D. in plant ecology. As he got into his studies, however, he became interested in theoretical questions.
"As an undergraduate, I read a number of great papers on evolutionary biology written by Robert Trivers, who was then at Harvard," Haig recalls. "My interest in genomic imprinting started with these papers. Trivers is now at Rutgers University, and since coming to America, we're gotten to be good friends."
For his Ph.D., earned in 1989, Haig did a theoretical thesis on the life cycles of vascular plants. He then went to Oxford University for two years of postdoctoral work. Afterwards, Pierce nominated him for the Harvard Society of Fellows.
Haig arrived at Harvard in 1992, and describes the fellowship as "a wonderful three years." He was appointed a tenured professor last year.
"David is a person of enormous integrity who is deeply thoughtful about ethical, political, and religious views of all kinds," comments Pierce. "Not only is he one of the most original evolutionary theoreticians of his generation, but he is genuinely kind and generous to everyone around him. Besides, he is fun to relax and have a drink with, and he tells marvelous stories."
Clerking couldn't hold him
Haig's road from undergraduate to tenured professor was not as straight as it is for most people. After earning his bachelor of science degree, he decided to take time out "to learn about other things in life." After working as a dishwasher, he landed a position as clerk for the New South Wales State Government.
"I had a rubber stamp and it cost people money for me to stamp their legal documents," he explained. "I learned a lot about the world, life, and people during the three years I took off. But, after a couple years of stamping documents, I decided that academia was a better place to be. It's not as carefree as the life of a clerk, but it's more intellectually stimulating."
Now that he has reached a peak in academia, Haig says he "would like to get back to plants. Genomic imprinting occurs in them, too," he points out. "There is also a lot of loose ends in my thesis work, fascinating things about plant life cycles that I'd like get back to."
College of Pharmacy/Toxicology - Faculty Candidate
Yu-an Cao, Ph.D., Research Associate
Neonatal and Developmental Medicine, Stanford University School of Medicine
Thursday, March 29, 11:00am in PHR 4.114
Host: Dr. Shawn Bratton
"Stem cell stress response regulated by heme oxygenase-1"
Next week's Toxicology seminar will be given by a Pharmacology & Toxicology faculty candidate. Dr. Yu-an Cao, Research Associate in the Neonatal and Developmental Medicine Division at Stanford University School of Medicine, will be speaking on "Stem cell stress response regulated by heme oxygenase-1" The seminar will be in PHR 4.114 at 11:00 on Thursday, March 29.
The seminar will be televised to Science Park for those of you not being able to make it to Austin for the talk.
Speaking of Biology
Pharmacology & Toxicology faculty candidate
Dr. Yu-an Cao
Research Associate, Neonatal and Developmental Medicine Division,
Stanford University School of Medicine
"Stem cell stress response regulated by heme oxygenase-1."
Thursday, March 29 - 11:00 a.m. - PHR 4.114
Speaking of Biology
Spring 2007 Lorene Morrow Kelly Distinguished Lecture co-sponsored by the
School of Biological Sciences and the Section of Integrative Biology
Dr. David Haig
Department of Organismic and Evolutionary Biology, Harvard University
"Genomic imprinting and social behavior."
Thursday, March 29 - 4:00 p.m. - ACES 2.302 - Reception to follow in O's courtyard.
Host: Dr. Mike Ryan
Speaking of Biology
Institute for Cellular and Molecular Biology
Julian I. Schroeder, Ph.D.
Professor in Plant Sciences, University of California, San Diego
"Guard Cell and Ion Channel Signaling; CO2, Abscisic Acid and Calcium Specificity Transduction."
Thursday, March 29 - 4:00 p.m. - MBB 1.210
Speaking of Biology
Section of Neurobiology Recruitment Seminar
Rene Renteria, Ph.D.
University of California, San Francisco
"Chalk Talk."
Wednesday, March 28 - 11:00 a.m. - NMS 1.120
Speaking of Biology
Geological Sciences Dissertation Defense
Dennis Ruez
"Effects of climate change on mammalian fauna composition and structure during the advent of North American continental glaciation in the Pliocene."
Wednesday, March 28 - 2:00 p.m. - GEO 6.208
Speaking of Biology
Marine Science Institute-Schweppe Speaker
Dr. Ed Malkiel
Johns Hopkins University
"Holographic Views of the Plankton World."
Wednesday, March 28 - 3:45 p.m. - Visitors Center Auditorium at the Marine Science Institute,
Port Aransas, TX
For directions to the Marine Science Institute, go to: http://msi40.utmsi.utexas.edu/institute/maps.htm
Speaking of Biology
Waggoner Center for Alcohol Addiction & Research/Section of Neurobiology
Recruitment Seminar
Veronica Alvarez, Ph.D.
Research Fellow in Neurobiology, Harvard Medical School
"Chalk Talk."
Tuesday, March 27 - 12:00 p.m. - NMS 1.120
Host Adron Harris, Ph.D.
Speaking of Biology
Section of Molecular Cell and Developmental Biology
Dr. William Bement
Department of Zoology, University of Wisconsin-Madison
"Control of Wound Repair and Cell Division by RHO GTPase Activity Zones."
Tuesday, March 27 - 4:00 p.m. - MBB 1.210 - Refreshments will be served at 3:30.
Speaking of Biology
Section of Neurobiology Recruitment Seminar
Rene Renteria, Ph.D.
University of California, San Francisco
"Building receptive fields: The mGluR6 KO mouse reveals a novel response of the retinal OFF pathway."
Tuesday, March 27 - 4:00 p.m. - ACE 2.402
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-Departmental Seminar Series
David Barnes, Ph.D.
Mount Desert Island Biological Laboratory, Salisbury Cove, Maine
"In vitro culture of freshwater and marine fish models: Tools for cell and molecular biology."
Monday, March 26 - 11:00 a.m. - Harrison Auditorium, Pickle Conference Center, Science Park, Smithville, TX
For directions to the Science Park, go to: http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Population Biology
Edward LeBrun
Postdoctoral Fellow, Section of Integrative Biology, UT-Austin
"Dynamic expansion of recently introduced populations of fire ant parasitoids (Diptera: Phoridae)."
Monday, March 26 - 12:00 p.m. - MBB 1.210
Host: Dr. Larry Gilbert
Speaking of Biology
Center for Perceptual Systems
Chen Yu, Ph.D.
Department of Psychological and Brain Sciences, Indiana University
"Multimodal Statistical Learning: Linking Words to World."
Monday, March 26 - 12:00 p.m. - SEA 4.244 - Reception with refreshments at 11:30 a.m.
Speaking of Biology
Center for Nonlinear Dynamics
William H. Press, Ph.D.
Section of Integrative Biology & Institute for Computational and Engineering Sciences, UT-Austin
"Entropy Distances, Polygraphic Models, and Clustering of Genomic Sequences."
Monday, March 26 - 1:00 p.m. - RLM 11.204
Speaking of Biology
Biochemistry Division Seminar
Roger Goody, Ph.D.
Director of the Max-Planck Instutute of Molecular Physiology, Dortmund, Germany
"The structural and mechanistic basis for the regulation of intracellular vesicular transport by Rab GTPases."
Monday, March 26 - 1:30 p.m. - WEL 2.122
Host: Kenneth A. Johnson, Ph.D.
Speaking of Biology
Waggoner Center for Alcohol Addiction & Research/Section of Neurobiology
Recruitment Seminar
Veronica Alvarez, Ph.D.
Research Fellow in Neurobiology, Harvard Medical School
"Regulation of synaptic structure and function by the Tuberous Sclerosis Complex pathway."
Monday, March 26 - 4:00 p.m. - MBB 1.210
Host Adron Harris, Ph.D.
UTCS Colloquium/Architecture
Tom Puzak, IBM T.J. Watson Research Center
Monday, March 26, 2007 3:30 p.m. - ACES 2.402
Host: Yale Patt
"An Analysis of the Effects of Miss Clustering on the Cost of a Cache Miss"
Talk Abstract:
A new technique, called Pipeline Spectroscopy, is described that allows pipeline delays to be monitored and analyzed in detail. We use this technique to measure the cost of each cache miss. The cost of a miss is displayed (graphed) as a histogram, which represents a precise readout showing a detailed visualization of the cost of each cache miss throughout all levels of the memory hierarchy. We call the graphs 'spectrograms' because they reveal certain signature characteristics of the processor's memory hierarchy, the pipeline, and the miss pattern itself. Cache miss spectrograms are produced by analyzing misses according to the miss cluster size, and comparing instruction sequences and execution times that occurred near the miss cluster in a 'finite cache' simulation run to the same set of instructions and execution times in an 'infinite cache' run, then calculating the difference in run times. We show that in a memory hierarchy with N cache levels (L1, L2, ..., LN, and memory) and a miss cluster of size C, there are (C+N) choose C possible clusters of miss penalties. This represent all possible sums from all possible combinations of the miss latencies from each level of the memory hierarchy (L2, L3, ... Memory) for a given cluster size. Additionally, a theory is presented that describes the shape of a spectrogram, and we use this theory to predict the shape of spectrograms for larger miss clusters. Detailed analysis of a spectrograph leads to much greater insight in pipeline dynamics, including effects due to prefetching, and miss queueing delays.
Speaker Bio:
Thomas R. Puzak received a B. S. in Mathematics and M. S. in Computer Science from the University of Pittsburgh and a Ph. D. in Electrical and Computer Engineering from the University of Massachusetts. Since joining IBM he has spent over thirty years working in IBM Research. While at IBM he received Technical Achievement, Outstanding Contribution, and Innovation Awards, served as Chairman of the Computer Architecture Special Interest Group at the T. J. Watson Research Center and holds more than 30 patents, on processor and memory design.
The Computer Architecture Seminar Series is sponsored jointly by the Departments of Computer Science and Electrical & Computer Engineering and is supported by a grant from AMD.
CPS Seminar
Chen Yu, Ph.D., Assistant Professor, Dept of Psychological and Brain Sciences, Cognitive Science Program and Department of Computer Science, Indiana University
March 26, 12:00, SEA 4.244
Reception with Refreshments at 11:30 AM
Host: Dana H. Ballard
"Multimodal Statistical Learning: Linking Words to World"
UTCS Colloquium/Programming Languages Seminar
Martin Burtscher, Cornell University
March 26, 2007, 12:15p.m. - 1:15p.m., TAY 3.128 - East wall (chalkboard)
Host: Keshav Pingali
"Multicore and Other New Approaches to Reduce the Data Access Latency"
Talk Abstract:
High-end microprocessors are poorly utilized because they often have to wait for data to be delivered. This talk presents several novel hardware and software ideas that alleviate this inefficiency by reducing the time it takes to access the data.
First, we briefly discuss two latency-hiding techniques, load-value prediction and source code scheduling.
Second, we present an innovative multicore approach called Future Execution to lower the access latency. Future Execution pairs up cores and transparently and continuously converts the running program threads into helper threads that are streamed into the alternate cores.
Third, we introduce a high-speed lossless compression algorithm to decrease the data size in real time. We conclude the talk with an outlook into the future.
ICES/CS Seminar
Rajit Manohar, Cornell University
Friday, March 23, 2007 3:00 p.m. - 4:00 p.m. - ACE 6.304
Host: Keshav Pingali
"Reconfigurable Asynchronous Logic"
Talk Abstract:
We present the design of an asynchronous FPGA (AFPGA) architecture and its measured performance over a wide range of temperatures and operating voltages. The AFPGA is implemented as a configurable dataflow architecture, and attains a performance that significantly exceeds the performance of commercial FPGAs as well as any reported result in the literature without any increase in its energy per operation. We also discuss some issues that arise in the synthesis of high-level designs to the AFPGA architecture.
Speaking of Biology
Physiology & Behavior
Dr. Arthur Arnold, UCLA
"Sex chromosome dosage compensation is not for the birds."
Friday, March 23 - 12:00 p.m. - PHR 4.114
Host: Dr. David Crews
Speaking of Biology
Jean Andrews Visiting Professor in International Nutrition:
Henry J. Thompson, Ph.D.
Director, Cancer Prevention Laboratory, Colorado State University
"Plant Foods and Health in a Global Context."
Friday, March 23 - 2:00 p.m. - GEA 105
Speaking of Biology
Section of Molecular Genetics and Microbiology Research in Progress
Makkuni Jayaram, PhD, Professor, Section of Molecular Genetics and Microbiology, UT-Austin
"The yeast Plasmid: an impostor chromosome?"
Friday, March 23 - 3:30 p.m. - MBB 1.210
Host: Liz Wyckoff
Speaking of Biology
Section of Integrative Biology & Section of Neurobiology Faculty Recruit
Anthony Leonardo
Harvard University
"Chalk Talk."
Thursday, March 22 - 11:00 a.m. - MBB 1.210
Speaking of Biology
Toxicology faculty candidate
Dr. Jiyong Liang, Postdoctoral Fellow, UT MD Anderson Cancer Center
"Autophagy at the crossroad of cancer cell death and survival."
Thursday, March 22 - 11:00 a.m. - PHR 4.114
Speaking of Biology
Section of Integrative Biology
Dr. Arthur Arnold, UCLA
"Sex chromosomes and sexual differentiation."
Thursday, March 22 - 2:00 p.m. - MBB 1.210
Host: Dr. David Crews
EDGE Student Scholar Seminar
Brian Smith, EDGE Center - Electrical and Computer Engineering
March 22, 2007, 2:00p.m. - 3:00p.m., ACES 2.402
Host: Sriram Vishwanath
"Capacity of Erasure Networks"
Talk Abstract:
In this talk, we study the capacity of several novel models of erasure networks. An erasure channel is a communication model in which every input symbol is either 1) correctly and identically received at the output or 2) appears at the output as an "error" symbol, giving us no information about which choice of symbol was intended. Specifically, if a valid symbol is recieved, then there is no ambiguity about which symbol was transmitted. A memoryless erasure network is one in which defining characteristic is that each channel between any two nodes is an independent erasure channel. The various models that we explore differ in the absence or presence of interference at either the transmitters, the receivers, or both; and in the availability of feedback at the transmitters. We show several mathematicaly interesting capacity results for such kinds of networks.
Speaking of Biology
Ecology, Evolution, and Behavior Dissertation Defense
Anna Himler
"Evolutionary Ecology and Natural History of Fungus-Growing Ants:
Host-switching, Divergence and Asexuality."
Wednesday, March 21 - 10:00 a.m. - GEA 125
Speaking of Biology
Section of Neurobiology Recruitment Seminar
Stephan Brenowitz, Ph.D., Harvard Medical School
"Chalk talk."
Wednesday, March 21 - 12:00 p.m. - NMS 1.120
Speaking of Biology
Jean Andrews Visiting Professor in International Nutrition:
Henry J. Thompson, Ph.D., Director, Cancer Prevention Laboratory, Colorado State University
"Caloric balance, energy sensing and cancer risk."
Wednesday, March 21 - 3:00 p.m. - PHR 4.114
Please reserve a seat for this talk by contacting Kathy McWilliams
(kathymcw@mail.utexas.edu)
Host: Dr. Steve Hursting
Speaking of Biology
Section of Integrative Biology & Section of Neurobiology Faculty Recruit
Anthony Leonardo, Harvard University
"Complex dynamics and simple population codes in a retinal target tracking circuit."
Wednesday, March 21 - 3:00 p.m. - ACE 2.302
Speaking of Biology
Behavioral Neuroscience-Faculty Recruit
Marle Monfils
"Targeted Disruption of Fear Memory Reconsolidation."
Wednesday, March 21 - 3:00 p.m. - SEA 4.244
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-Faculty Seminar Series
Mark Bedford, Ph.D. , UT MD Anderson Cancer Center Science Park - Research Division
"Using proteomic approaches to understand proein methylation."
Wednesday, March 21 - 3:30 p.m. - Harrison Auditorium, Pickle Conference Center, Science Park,
Smithville, TX
For directions to the Science Park, go to: http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Section of Molecular Genetics and Microbiology
Dr. Timothy Murphy
Professor of Medicine and Microbiology, Chief, Infectious Diseases,
University at Buffalo - State University of New York
"Pathogenesis of Haemophilus influenzae Infection, an Exclusively Human Pathogen."
Wednesday, March 21 - 4:00 p.m. - ESB 223 - Refreshments served.
Host: Erin Murphy
Speaking of Biology
Jean Andrews Centennial Visiting Professorship in Tropical and Economic Botany.
Dr. Will McClatchey, University of Hawaii - Manoa
"Using Traditional Knowledge of Plants as a Measure of Local Biodiversity."
Wednesday, March 21 - 7:00 p.m. - Lady Bird Johnson Wildflower Center, 4801 La Crosse Avenue,
Austin, Texas 78739
(Visitor Reception at 6:00 p.m.)
For directions please go to: http://www.wildflower.org/?nd=directions
Speaking of Biology
Wellness Symposium continues
Tuesday, March 20 - 8:30 a.m. to 2:30 p.m. - Thompson Conference Center
For more information and to register, please go to:
http://www.utsystem.edu/hea/wellness/
Host: Dr. Joseph McCormick, Dean of the UT School of Public Health, Regional Campus at Brownsville
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-DNA Repair Group Series
Dr. Paul Wilson, Dr. Zac Purcell, Dr. Karin Scarpinato
Young Investigator Showcase:
1) "DNA double strand break repair capacity after low dose Ionizing radiation."
2) "Yeast DNA polymerase epsilon in DNA replication."
3) "PMS2 elevation in prostate cancer."
Tuesday, March 20 - 11:30 a.m. - Harrison Auditorium, Pickle Conference Center, Science Park, Smithville, TX
For directions to the Science Park, go to:
http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Jean Andrews Centennial Visiting Professorship in Tropical and Economic Botany.
Dr. Will McClatchey, University of Hawaii - Manoa
"Ethnobotanical Basis of Plant Classification Systems in Polynesia."
Tuesday, March 20 - 12:00 p.m. - BIO 214
Speaking of Biology
Imaging Research Center - Seminars in Surface Based Morphometry
David Salat, Ph.D.
"Neuroimaging Studies of Aging and Dementia with SBM and Diffusion Tensor Imaging."
Tuesday, March 20 - 3:30 p.m. - SEA 2.108
Speaking of Biology
Section of Molecular Cell and Developmental Biology
Dr. Ray Keller, Department of Biology, University of Virginia
"The Patterning, Cell Motility, And Biomechanics Of Several Strategies Of Amphibian Gastrulation."
Tuesday, March 20 - 4:00 p.m. - MBB 1.210 - Refreshments will be served at 3:30.
Host: Ryan Gray
Speaking of Biology
Section of Neurobiology Recruitment Seminar
Stephan Brenowitz, Ph.D., Harvard Medical School
"Retrograde modulation of synaptic transmission by endocannabinoids."
Tuesday, March 20 - 4:00 p.m. - ACE 2.402
Speaking of Biology
Physics Pizza Seminar
Ernst-Ludwig Florin, UT-Austin
"Biophysics Research at the Center For Nonlinear Dynamics!"
Tuesday, March 20 - 5:00 p.m. - RLM 7.104
Department of Computer Sciences - Faculty Candidate
Swarat Chaudhuri - University of Pennsylvania
Tuesday, March 20, 2007 11:00 a.m. - Noon
ACES 2.302
Host: Jayadev Misra
"Context-Sensitive Software Model Checking"
Talk Abstract:
Software model checking, an algorithmic, specification-driven approach to software analysis, has emerged as an active area of research in the last few years, producing a number of successful tools. While work in this area builds on the 25-year-old literature on model checking of finite-state systems, it has to grapple with several additional issues. A crucial one is that control flow of procedural programs depends on "contexts" defined by the call stack, so that any reasonably precise software model checker needs to analyze pushdown models of programs rather than finite-state ones.
In this talk, I address two main components of such "context-sensitive" model checking: requirement specification and algorithmic analysis. The first ---and main---story starts with the observation that temporal specification logics like the mu-calculus, while mainstays of traditional model checking, cannot specify "context-sensitive" program requirements such as: "A file is read before control leaves the current procedural context." The difficulty is that the mu-calculus is only as expressive as tree automata, and thus cannot reason about the nesting of contexts. A way to overcome this issue, I demonstrate, is to view a program as a generator not of a computation tree, but of a graph called a "nested" tree. Temporal logics interpreted on this new structure are now defined, and the model checking problem is re-phrased as: "Does the nested tree generated by a program satisfy a property?" Not only does this tweak let us state many new requirements, but it does so without changing the complexity of model-checking. There are other positives: for example, a fixpoint calculus on nested trees that we define allows symbolic model-checking and modular specifications, and has an automata-theoretic characterization similar to that for the mu-calculus.
Next I address the reachability problem for pushdown automata, an algorithmic problem central to software model checking that also shows up in contexts such as slicing, alias analysis, shape analysis, and type-based flow analysis. In a recent result, I have used a form of preprocessing to improve the thirty-something-years old cubic solution to this problem, also answering the question of whether its many applications suffer from an intrinsic "cubic bottleneck". I briefly sketch the technique, as well as suggest how the core idea of the algorithm may find general use in heuristic design for software analysis.
ICES SEMINAR
Tuesday, March 20, 2007 - 3:30 to 5:00 p.m. - ACES 6.304
Dr. Daniel S. Katz
Center of Computation and Technology, Louisiana State University
Host: Robert van de Geijn
Data-Oriented Distributed Computing for Science
Abstract:
As is becoming commonly known, there is an explosion happening in the amount of scientific data that is publicly available. One challenge is how to make productive use of this data. This talk will discuss some parallel and distributed computing projects, centered around virtual astronomy, but also including ocean/coastal modeling. It will look at some specific projects from the past, including Montage, Grist, OurOcean, and SCOOP, and will discuss the distributed computing, Grid, and Web-service technologies that have successfully been used in these projects.
Contact: Robert van de Geijn, rvdg@cs.utexas.edu
Professor, Department of Computer Sciences, The University of Texas at Austin
(512) 471-9720 - http://www.cs.utexas.edu/users/rvdg
Speaking of Biology
Imaging Research Center - Seminars in Surface Based Morphometry
"Introduction to SBM and the use of Freesurfer."
Monday, March 19 - 9:00 a.m. - 3rd floor Alamo Room, MCC building, Pickle Campus West
Speaking of Biology
Wellness Symposium
Keynote Speaker at 11:30 a.m.:
Darwin R. Labarthe, M.D., M.P.H., Ph.D.
Director, Division for Heart Disease & Stroke Prevention, National Ctr for Chronic Disease Prevention & Health Promotion, CDC
Monday, March 19 - 9:30 a.m. to 6:30 p.m. - Thompson Conference Center
For more information and to register, please go to: http://www.utsystem.edu/hea/wellness/
Host: Dr. Joseph McCormick, Dean of the UT School of Public Health, Regional Campus at Brownsville
Speaking of Biology
Section of Integrative Biology (Neuroethology faculty recruit)
Kim Hoke, Postdoc, Section of Integrative Biology, UT-Austin
"Brain networks mediating reproductive decision making."
Monday, March 19 - 10:00 a.m. - ACE 2.302
Speaking of Biology
Population Biology
Alex Wild, University of Arizona
"Can 18th and 21st century science get along? The fate of taxonomy in the genomic era
(as revealed by Linepithema ants)."
Monday, March 19 - 12:00 p.m. - MBB 1.210
Host: Dr. Ulrich Mueller
Speaking of Biology
Center for Perceptual Systems
Robert H. Wurtz, Ph.D.
Laboratory of Sensorimotor Research, National Eye Institute, National Institutes of Health
"Corollary Discharge and Perceptual Stability."
Monday, March 19 - 12:00 p.m. - SEA 4.244 - Reception with refreshments at 11:30 a.m.
Speaking of Biology
Jean Andrews Centennial Visiting Professorship in Tropical and Economic Botany.
Dr. Will McClatchey
University of Hawaii - Manoa
"Impacts of Climate Change on Atoll Cultures of the Central Pacific."
Monday, March 19 - 4:00 p.m. - GRG 102
Speaking of Biology
Section of Neurobiology
Karl Kandler, Ph.D., University of Pittsburgh
"Developmental reorganization of inhibitory sound localization circuits."
Monday, March 19 - 4:00 p.m. - MBB 1.210
Host: Dr. Nace Golding
UTCS Colloquium/Architecture
Dan Sorin, Duke University
Monday, March 19, 2007 3:30 p.m. - ACES 2.402
Host: Steve Keckler
"Comprehensive Detection of Errors in Multithreaded Memory Systems"
Talk Abstract:
Multithreaded architectures, including multicore processors and multithreaded uniprocessors, are becoming ubiquitous. Our goal is to detect all possible errors in the memory systems of these machines, without resorting to large amounts of expensive and power-hungry redundancy. Because correct operation of the memory system is defined by the memory consistency model, we can detect errors by checking if the observed memory system behavior deviates from the specified consistency model. We have designed a framework for dynamic verification of memory consistency (DVMC), and this framework applies to all existing commercial consistency models. Our DVMC framework consists of mechanisms to dynamically verify three invariants that we have proven to be equivalent to memory consistency. We have developed an implementation of the framework for the SPARCv9 architecture, and we have experimentally evaluated its performance using full-system simulation of commercial workloads.
Speaker Bio:
Daniel J. Sorin is an assistant professor of Electrical and Computer Engineering and of Computer Science at Duke University. His research interests include dependable computer architecture and system design. He received a PhD and MS in electrical and computer engineering from the University of Wisconsin, and he received a BSE in electrical engineering from Duke University. He is the recipient of an NSF Career Award and a Warren Faculty Scholarship at Duke.
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-Departmental Seminar Series
David Brown, Ph.D.
Asuragen, Inc., Austin, Texas
"Micro RNAs."
Fri., March 16 - 9:00 a.m. - Harrison Auditorium, Pickle Conf. Center, Science Park, Smithville, TX
For directions to the Science Park, go to:
http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Marine Science Institute
Dr. Lee Fuiman
Director, Marine Science Institute
"Underwater Behavior of Antarctica Seals."
Thurs., March 15 - 7:00 p.m. - Visitors Center Auditorium at the Marine Sci. Inst., Port Aransas, TX
For directions to the Marine Science Institute, go to:
http://msi40.utmsi.utexas.edu/institute/maps.htm
Department of Computer Sciences - Artificial Intelligence
Dr. Rong Jin, Computer Science and Engineering Dept., Michigan State University
Wednesday, March 14, 2007, 11:00 a.m. - Noon - ACES 6.304
Host: Prof. Joydeep Ghosh
"Generalized Maximum Margin Clustering and Unsupervised Kernel"
Talk Abstract:
Maximum margin clustering extends the theory of support vector machine to unsupervised learning, and has shown promising performance in recent studies. However, it has three major problems that question its application of real-world applications: (1) it is computationally expensive and difficult to scale to large-scale datasets; (2) it requires data preprocessing to ensure the clustering boundary to pass through the origins, which makes it unsuitable for clustering unbalanced dataset; and (3) its performance is sensitive to the choice of kernel functions. In this paper, we propose the "Generalized Maximum Margin Clustering" framework that addresses the above three problems simultaneously.
The new framework generalizes the maximum margin clustering algorithm in that (1) it allows any clustering boundaries including those not passing through the origins; (2) it significantly improves the computational efficiency by reducing the number of parameters; and (3) it automatically determines the appropriate kernel matrix without any labeled data. Our empirical studies demonstrate the efficiency and the effectiveness of the generalized maximum margin clustering algorithm. Furthermore, in this talk, I will show the theoretical connection among the spectral clustering, the maximum margin clustering and the generalized maximum margin clustering.
Speaker Bio:
Dr. Rong Jin is an Assistant Prof. of the Computer Science and Engineering Dept. of Michigan State University since 2003. He is working in the areas of statistical machine learning and its application to information retrieval. Dr. Jin holds a B.A. in Engineering from Tianjin University, an M.S. in Physics from Beijing University, and an M.S.and Ph.D. from School of Computer Science of Carnegie Mellon University.
Department of Computer Sciences - Artificial Intelligence
Hermann Helbig/University of Hagen, Germany
March 9, 2007 - 11:00 a.m. - ACE 6.304
Host: Bruce Porter
"Multilayered Extended Semantic Networks as a Knowledge Representation Paradigm and Interlingua for Meaning Representation"
The talk gives an overview of Multilayered Extended Semantic Networks (abbreviated MultiNet), which is one of the most comprehensively described knowledge representation paradigms used as a semantic interlingua in large-scale NLP applications and for linguistic investigations into the semantics and pragmatics of natural language.
As with other semantic networks, concepts are represented in MultiNet by nodes, and relations between concepts are represented as arcs between these nodes. Additionally to that, every node is classified according to a predefined conceptual ontology forming a hierarchy of sorts, and the nodes are embedded in a multidimensional space of layer attributes and their values.
MultiNet provides a set of about 150 standardized relations and functions which are described in a very concise way including an axiomatic apparatus, where the axioms are classified according to predefined types. The representational means of MultiNet claim to fulfill the criteria of universality, homogeneity, and cognitive adequacy. In the talk, it is also shown, how MultiNet can be used for the semantic representation of different semantic phenomena.
To overcome the quantitative barrier in building large knowledge bases and semantically oriented computational lexica, MultiNet is associated with a set of tools including a semantic interpreter NatLink for automatically translating natural language expressions into MultiNet networks, a workbench LIA for the computer lexicographer, and a workbench MWR for the knowledge engineer for managing and graphically manipulating semantic networks.
The applications of MultiNet as a semantic interlingua range from natural language interfaces to the Internet and to dedicated databases, over question-answering systems, to systems for automatic knowledge acquisition.
Speaker Bio:
Hermann Helbig is Professor at the University of Hagen, Germany, and head of the chair Intelligent Information and Communication Systems. He received his Dr.rer.nat. (PhD) in 1976 in Automatic Symbolic Formula Manipulation and his Dr.rer.nat.habil. (Habilitation) in 1986 in Knowledge Representation. His experiences in AI research cover a period of more than 30 years. His main contributions lie in the fields of question answering (question answering system FAS-80), natural language interfaces to data bases (NLI-AIDOS), word-class controlled functional analysis (WCFA), knowledge representation (MultiNet paradigm), and computational lexicography (semantically based computational lexicon HaGenLex). He is author of several monographs in AI, his last book relevant to the talk is "Knowledge Representation and the Semantics of Natural Language."
His research interests cover issues in Natural Language Processing, Computational Lexicography, Knowledge Representation and Management, Semantics of NL, and Electronic Distance Teaching in AI.
Speaking of Biology
Hydrology Brown Bag Seminar
Mary Poteet
School of Biological Sciences, UT-Austin
"The Barton Springs Salamander."
Friday, March 9 - 12:00 p.m. - GEO 3.222
Speaking of Biology
Physiology & Behavior
Di Wu
College of Pharmacy, UT-Austin
"Age-related in sex steroids and receptors in female rats."
Friday, March 9 - 12:00 p.m. - PHR 4.114
Host: Dr. David Crews
Speaking of Biology
Integrative Graduate Education and Research Traineeship Program
Stuart Foster, Ph.D.
Professor and Associate Chair, Department of Medical Biophysics, University of Toronto
"Micro-Ultrasound in the Land of Bioresearch."
Friday, March 9 - 1:00 p.m. - ACE 2.402
Host: Stas Emelianov
Speaking of Biology
Lady Bird Johnson Wildflower Center Nature Nights: An Evening of Fun Family Learning
John Young
Texas Parks & Wildlife
"Wildcats of Texas."
Friday, March 9 - 6:00-9:00 p.m. - Lady Bird Johnson Wildflower Center, 4801 La Crosse
Avenue, Austin, Texas 78739
For more information please go to: http://www.wildflower.org/?nd=nature
Computer Sciences Seminar
Sunay Tripathi, Sun Microsystems (FoCS)
Thursday, March 8, 2007 - 2:00 p.m. - ACES 2.402
Host: Greg Lavender
"Virtualizable Architecture for High Performance Network Stack"
Talk Abstract:
The Networking stack in Solaris 10 uses a new architecture for doing network processing where the NIC is controlled by the network and the transport layers creating a per CPU vertical perimeter. The network stack is able to schedule the receive-side packet processing by dynamically controlling the rate of packet arrival from individual receive rings on the NIC. The architecture minimizes context switches and allows processing of packets without losing CPU affinity or contending for any locks.
The network processing for a connection is performed from a vertical perimeter, which is implemented by a serialization queue and consists of one or more threads bound to a CPU for better locality.
There is, at most, one queuing, and a packet once picked up for processing is processed all the way to the socket layer on the inbound case, and all the way to the NIC on the outbound case without needing to contend for additional locks or switch context.
The stack also provides the building blocks for network virtualization and resource control by creating virtual stacks around any service (HTTP, HTTPS, FTP, NFS, etc.), protocol (TCP, UDP, SCTP, etc.), or Virtual machines like Containers or Xen.
Each virtual stack can be assigned its own priority and band-width on a shared NIC without causing any performance degradation. The architecture dynamically manages priority and bandwidth resources, and can provide better defense against denial-of-service attacks directed at a particular service or virtual machine by isolating the impact just to that entity. The virtual stacks are separated by means of H/W classification engine such that traffic for one stack does not impact other virtual stacks.
Speaker Bio:
Sunay Tripathi is a Distinguished Engineer at Sun Microsystems, where he works on the Solaris Core Operating Systems team.
Department of Computer Sciences - Colloquium
Greg Lavender, University of Texas-Austin
Thursday, March 8, 2007 - 5:00 p.m. - 6:00 p.m. - ACES 6.304
Host: GRACS
"GRACS Development Talk: Startups"
Many graduate students have expressed interest in learning more about using their graduate degree in industry and specifically what it is like to start a company. Toward this end, GRACS is hosting a talk by Professor Greg Lavender on his experiences in industry.
Professor Lavender worked at an industry R&D lab and then started his own company, which he later morphed into a second one. Then he sold that company to a larger company, and finally helped this larger company get acquired by Sun Microsystems.
UTCS Colloquium/EDGE Distinguished Speaker Lecture Series
Sriram Vishwanath, Department of Electrical and Computer Engineering
March 8, 2007 - 2:00p.m. - 3:00p.m. - ACES 2.402
Host: EDGE Center
"Fundamental Limits of Wireless Networks"
Talk Abstract:
As the demand for ?anytime-anywhere? connectivity grows in our society, knowing the limits on the performance of these systems is invaluable. Capacity of wireless networks is an extensively studied yet elusive problem that lies at the intersection of many distinct fields of research. The principle issue is that any one field lacks all the appropriate tools needed to tackle this problem in its entirety. This talk will elaborate on the progress made on different fronts of this problem, with the ultimate goal of building a compelling theory that captures all aspects of the capacity of these networks. Specifically, we will discuss work done by members of the LINC group in this talk. Topics will include: Cognitive Radio and Interference Networks, Resource Allocation in Multiple Antenna Systems and Capacity of Erasure Networks.
Speaking of Biology
Behavioral Neuroscience Talk-Faculty Recruit
Donna Maney
Department of Psychology, Emory University
"Hormones and Love Songs: Integration of Endocrine and Auditory Responses to Courtship Signals."
Thursday, March 8 - 12:00 p.m. - SEA 4.244
Speaking of Biology
Center for Learning and Memory-Faculty Recruit
Joseph Manns
Center for Memory and Brain, Boston University
"Chalk Talk."
Thursday, March 8 - 12:00 p.m. - NMS 1.120
Host: Dr. Daniel Johnston
Speaking of Biology
Section of Integrative Biology
Richard Mack
Washington State University
"Invasive Species."
Thursday, March 8 - 2:00 p.m. - MBB 1.210
Host: Dr. Don Levin
Department of Computer Sciences - Artificial Intelligence
Mark Steedman, University of Edinburgh
Wednesday, March 7, 2007 - 11:00 a.m. - Noon - ACES 2.402
Host: Jason Baldridge
"The Computational Problem of Natural Language Acquisition"
The talk reviews work-in-progress on language acquisition in children and robots using combinatory categorial grammar (CCG), building on work by Siskind, Villavicencio, and Zettlemoyer, among others.
CCG is a theory of grammar in which all language-specific grammatical information resides in the lexicon. A small universal set of strictly type-driven, non-structure dependent, syntactic rules (based on Curry's combinators B, S, and T) then "projects" lexical items into sentence-meaning pairs. The task that faces the child in the earliest stages of language acquisition can therefore be seen as learning a lexicon on the basis of exposure to (probably ambiguous, possibly somewhat noisy) sentence-meaning pairs, given this universal combinatory "projection principle", and a mapping from semantic types to the set of all universally available lexical syntactic types.
The talk argues that a very simple statistical model allows children to arrive at a target lexicon without navigation of subset principles, or attention to any attendant notion of trigger other than the notion "reasonably short sentence in a reasonably understandable situation". The model explains the pattern of errors that have been found in elicitation experiments. The linguistic notion of "parameter" appears to be redundant to this process.
The talk goes on to consider some more general implications of the theory, including its application to the phenomenon of "syntactic bootstrapping," touching on the question of the prelinguistic origin of the combinatory projection principle itself.
Speaker Bio:
Mark Steedman is Professor in the School of Informatics at the University of Edinburgh. He received his PhD from the University of Edinburgh in 1973. He came to Edinburgh in 1998 from the University of Pennsylvania, where he was Professor in the Department of Computer and Information Science. He is a Fellow of the American Association for Artificial Intelligence, a Fellow of the Royal Society of Edinburgh, and a Fellow of the British Academy.
His research interests cover issues in computational linguistics, artificial intelligence, computer science, and cognitive science, and their applications in practical systems, including syntax and semantics of natural language, wide-coverage parsing, comprehension of natural language by humans and by machine, and the role of intonation in spoken language generation and analysis. Some of his research concerns the analysis of music by humans and machines. He has acted as advisor for twenty-four PhDs.
The Austin Forum (www.austinforum.org)
When: Wednesday, March 7, 2007 @ 6:30 p.m.
Where: J.J. Pickle Research Campus - Research Office Complex (Jackson School of Geosciences & Texas Advanced Computing Center's new building) Seminar Room 1.603
The Texas Advanced Computing Center (TACC) and the Austin Forum invite you to attend a participatory talk by Dr. Cynthia Schneider and Mr. Timothy Pope entitled "Technology in the Classroom: Tradition versus Innovation". As leaders in mathematics education in Texas, Schneider and Pope will discuss how to use technology in the mathematics classroom. What does technology look like when it aids the learning of specific content? Why and when might technology interfere with learning content? Is technology the answer to the rising costs of education?
If you plan to attend, please take the following survey in advance:
1. Go to: http://survey.keypress.com/web/surveyTakeForm.php?id=263
2. Login in as a student with the following: Username: AustinForum;
Password: austin.
3. Click on "Surveys".
4. Click on the pencil icon on the row titled "Austin Forum Survey."
5. Take survey and click "Submit" when done.
The mission of The Austin Forum is to promote awareness of issues and opportunities in our community and to enrich lives. The Forum invites distinguished professionals and leaders to speak on topics related to science and technology and how they impact society.
Learn more about the Austin Forum's upcoming events at: www.austinforum.org.
** This event is free and open to the public; complimentary food and drink will be provided prior to the talk @ 6:00 p.m. **
Speaking of Biology
Forum for Artificial Intelligence
Mark Steedman
Professor, University of Edinburgh
"The Computational Problem of Natural Language Acquisition."
Wednesday, March 7 - 11:00 a.m. - ACE 2.402
Speaking of Biology
UT M.D. Anderson Cancer Center Science Park-Hogg Seminar Series
John Petrini, Ph.D.
Memorial Sloan-Kettering Cancer Center New York, NY
"Genetic analysis of chromosome break metabolism: Suppression of
malignancy and sensitivity to DNA damage."
Wednesday, March 7 - 11:00 a.m. - Harrison Auditorium, Pickle Conference Center, Science
Park, Smithville, TX
For directions to the Science Park, go to:
http://sciencepark.mdanderson.org/about/location/
Speaking of Biology
Center for Learning and Memory-Faculty Recruit
Joseph Manns
Center for Memory and Brain, Boston University
"The hippocampus and memory for items and context."
Wednesday, March 7 - 3:00 p.m. - SEA 4.244
Host: Dr. Daniel Johnston
Speaking of Biology
Section of Molecular Genetics and Microbiology
Jeannine Brady, Ph.D.
Assistant Professor, Oral Biology, College of Dentistry, University of Florida, Gainesville, FL
"Streptococcal surprises: an emerging story of protein secretion."
Wednesday, March 7 - 4:00 p.m. - ESB 223 - Refreshments served.
Host: Dr. George Georgiou
Department of Computer Sciences - Faculty Candidate
Aaron Bradley, Stanford University
Tuesday, March 6, 2007 - 11:00 a.m. - Noon - ACES 2.302
"Analyzing Properties of Systems"
As the complexity of and the dependence on engineered systems rises, correctness becomes ever more important. Verification aims to prove or to disprove that a system's implementation meets its specification. A specification asserts a set of properties that should hold on all executions of the system. Two areas of research are fundamental to verification: invariant generation and decision procedures. In this talk, I describe progress in both.
I first present a strategy for letting properties guide an invariant generation procedure, a form of static analysis. I then exhibit two instances of the strategy. The first augments generation of affine inequality invariants to be property-directed. For the second instance, I introduce a procedure for generating clausal invariants of finite-state systems such as hardware circuits and show how to make it property-directed.
Arrays are ubiquitous data structures in software and in hardware specifications. I present a decision procedure for a fragment of a theory of arrays that allows some quantification. Besides being expressive, this fragment is interesting because it lies on the edge of decidability: natural and simple extensions produce undecidable fragments.
Finally, I briefly discuss my work with Zohar Manna on developing a new undergraduate course at Stanford. Our course and accompanying forthcoming text, both entitled "The Calculus of Computation", cover first-order logic; decision procedures; and software specification, verification, and analysis.
Speaking of Biology
Section of Molecular Cell and Developmental Biology
Dr. Mary Ellen Lane
Rice University
"Growth and Patterning of the Vertebrate Forebrain."
Tuesday, March 6 - 4:00 p.m. - MBB 1.210 - Refreshments will be served at 3:30.
Host: Dr. John Wallingford
Department of Computer Sciences - Colloquium/Architecture
Hillery Hunter/ IBM T. J. Watson Research Center
March 5, 2007 3:30 p.m. - ACES 2.402
Host: Lizy John
"IBM eDRAM: What?s all the Fuss?"
As the "nano" era of microelectronics approaches, technologists have begun to predict the "end of scaling" for six-transistor SRAM. Though easily 50% of modern microprocessor silicon area is occupied by caches, a particularly long-standing debate has surrounded one dense storage alternative: embedded DRAM. This talk will shed light on the technology causes of the infamous memory wall, provide a tutorial on the technology behind eDRAM, and look at the architectural fundamentals of latency, density, and availability pertaining to use of SRAM replacements in future systems.
Speaker Bio:
Hillery Hunter is a Research Staff Member in the Exploratory Systems Architecture Department of IBM's T.J. Watson Research Center in Yorktown Heights, NY. Her current research focuses on next-generation cache design, leveraging advances in storage cells, arrays, and microarchitecture. She is interested in cross-disciplinary research, spanning circuits, microarchitecture, and compilers to achieve new solutions to traditional problems. She received the Ph.D. degree in Electrical Engineering from the University of Illinois, Urbana-Champaign in 2004.
The Computer Architecture Seminar Series is sponsored jointly by the Departments of Computer Science and Electrical & Computer Engineering and is supported by a grant from AMD.
Speaking of Biology
Imaging Research Center- Recruit Seminar
Neculai Archip, Ph.D.
Harvard Medical School and Brigham and Women's Hospital
"Medical Image Analysis for Image Guided Therapy."
Monday, March 5 - 11:00 a.m. - SEA 2.224
Host: Dr. Michael Domjan
Speaking of Biology
Population Biology
Nelson Guda
Environmental Science Institute, UT-Austin
"National Ecological Observatory Network."
Monday, March 5 - 12:00 p.m. - MBB 1.210
Speaking of Biology
Center for Perceptual Systems
Josef Rauschecker, Ph.D.
Department of Physiology and Biophysics, Georgetown University Medical Center
"Parallel Processing Streams in Primate Auditory Cortex."
Monday, March 5 - 12:00 p.m. - SEA 4.244<