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The Computer Science Colloquium Series is a forum for invited speakers, faculty, and graduate students to share research ideas. Everyone is invited to attend and participate. An up-to-date listing of the speakers and abstracts of their talks will be posted here. Please e-mail the colloquium committee if you are interested in speaking or know of someone who would be a good addition to our program. Thank you.
Colloquia are generally held every Thursday or Tuesday at 3:40 p.m. except during academic holidays. See below for specific times and topics. Refreshments will be served after every colloquium in the conference room, 225 Atanasoff Hall.
In some cases, the colloquium will start at 4.10 pm and refreshments will be served earlier starting at 3.30 pm. These colloquiums are marked with an asterisk (*) below.
Next Colloquia
There are no colloquia scheduled for the next 7 days. Please check below for future colloquia.
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Distinguished Lecture Series in Computer Science 2002-2003
The Department of Computer Science is pleased to host the Distinguished Lecture Series in Computer Science 2002-2003. For further information on the distinguished lecture series please visit this link .
Listing of Talks
Several other speakers have agreed to present but have not yet been scheduled. Potential dates for these talks are listed as "to be announced" in the table below. All other dates are open. Please contact one of us listed below if you are interested in speaking or know of a potential contributor to our series.
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Abstracts
1. Mouse Whole-Genome AssemblyXiaoqiu Huang
We have recently developed a DNA sequence assembly program (PCAP) and used PCAP to assemble a mouse whole-genome data set of 30 million sequences on a cluster of Compaq computers. In this talk, I will describe the PCAP program and present assembly results produced by PCAP on the mouse data.
2. A Simple and Practical Approach to Unit Testing: The JML and JUnit WayYoonsik Cheon
Writing unit test code is labor-intensive, hence it is often not done as an integral part of programming. However, unit testing is a practical approach to increasing the correctness and quality of software; for example, the Extreme Programming approach relies on frequent unit testing.
In this talk we present a new approach that makes writing unit tests easier. It uses a formal specification language's runtime assertion checker to decide whether methods are working correctly, thus automating the writing of unit test oracles. These oracles can be easily combined with hand-written test data. Instead of writing testing code, the programmer writes formal specifications (e.g., pre- and postconditions). This makes the programmer's task easier, because specifications are more concise and abstract than the equivalent test code, and hence more readable and maintainable. Furthermore, by using specifications in testing, specification errors are quickly discovered, so the specifications are more likely to provide useful documentation and inputs to other tools. We have implemented this idea using the Java Modeling Language (JML) and the JUnit testing framework, but the approach could be easily implemented with other combinations of formal specification languages and unit test tools.
This talk is based on a joint work with Prof. Gary T. Leavens. The work is supported in part by the NSF under grant CCR-0097907 and CCR-0113181. This work has appeared in the ECOOP 2002 conference, in Malaga, Spain, June 2002. More information on JML can be found at http://www.jmlspecs.org.
3. Exploiting large sequence databases to build the phylogenetic tree of life: problems, strategies and algorithmsMichael Sanderson
Biological species are related to one another by a pattern of ancestry and descent generally represented as a rooted phylogenetic tree. This tree includes upwards of 5 million species, but only a small fraction of this diversity has been captured in phylogenetic analysis to date. Large molecular sequence databases are a rapidly growing source of data for these studies; GenBank, for example, archives sequence information on over 100,00 species. Exploitation of these databases for phylogenetic purposes will require solving significant methodological and computational problems that are only now being identified. Given that it is neither practical nor informative to analyze the entire database at once, most of these problems relate to how the database should be partitioned, analyzed and then recombined to provide synthesis. This talk discusses three of these problems. First, single-copy genes must be separated from those in gene families, because the former are much more readily useful for species tree reconstruction than the latter. Second, optimal concatenations of genes must be found to maximize the sequence data per species used in any one analysis. Third, trees resulting from partially overlapping sets of species must be combined into phylogenetic supertrees that are larger than any of the input trees. The first problem is addressed using phylogenetic randomization tests. The second is addressed by a novel application of existing algorithms for finding maximal bicliques in bipartite graphs. The third is addressed by a relatively new suite of consensus-like algorithms on trees with partially overlapping label sets. All three problems are illustrated by reference to a set of 100,000 proteins from green plants, extracted from GenBank. From these, we characterize the information content of the database with respect to building comprehensive phylogenetic trees, provide upper bounds on the size of concatenated data sets, and lower bounds on the number of phylogenetic supertrees needed. 4. Grid Computing and Computational Science (Distinguished Lecture)Francine D. Berman
Information Infrastructure has become a first-class tool for computational science. Today, computational and data management resources are key enablers for modeling, analyzing, and visualizing scientific phenomena as well as for managing and mining immense amounts of scientific data. Over the last ten years, the ability to link computational and data storage resources as a "Grid" has provided a critical platform for enabling large-scale science and engineering disciplines. In this talk, we describe the state of the art of Grid Computing and discuss the challenges of building the Grid over the next ten years to support the science and engineering discoveries of the future.
5. Software Safety Analysis of a Flight Guidance SystemAlan Tribble
An aircraft's Flight Control System provides the capability to stabilize and control the aircraft. Two key elements of a Flight Control System are the Flight Guidance System that generates guidance commands and the Auto-Pilot that executes them. The Flight Guidance System is a software function composed of flight control laws, that determine the roll and pitch values needed to achieve the desired flight characteristics, and mode logic, that selects the appropriate flight control law for the given situation.
We developed a formal, executable model of the requirements for the mode logic of a Flight Guidance System and conducted a software safety analysis on the model. In particular, we conducted a Functional Hazard Assessment in order to identify the potentially hazardous conditions and a Fault Tree Analysis to identify general properties of the software that, if incorrectly performed, could lead to these hazardous conditions. From this list of general properties we then developed an itemized listing of specific safety-related properties required of the software. As a check of completeness, we then conducted a Failure Modes, Effects, and Criticality Analysis to propagate the specific failures back to the system level and verify that all hazardous conditions had been accounted for.
We will provide an overview of the bi-directional software safety analysis conducted on this system in order to illustrate the utility of applying these standard safety techniques to flight critical software. We will also summarize progress made to date in the use of formal methods, (model checkers and theorem provers), to verify the presence of the required safety properties in the software itself.
6. Computational Medicine: The Computer is my Doctor? (Distinguished Lecture)Piet de Groen
The computer was introduced in healthcare facilities to store and process demographic and financial data. At present, the content of the medical record is being transferred from paper to electronic media, with some facilities being paperless and others still partially paper-based. The physician reads and processes the data as needed during the medical decision-making process. However, the increasing complexity of the medical field and the flood of data expected to be generated by genomic tests will demand that data are preprocessed by computer algorithms before being presented to the physician. Such processing can be based on guidelines experience of experts converted to computer-based rules or on statistical analysis of the outcome of patients with similar characteristics mining of the data collected in large sets of electronic medical records. At Mayo Clinic Rochester, in collaboration with IBM, we have created a data warehouse that will allow us to store clinical as well as genomic data of millions of patients. In addition, we have created a search engine that can identify subsets of patients with specific features. Expansion of the data within the warehouse and development of new algorithms to analyze and mine across all types of data are the focus of next steps in the collaboration. Eventually, this may lead to computationally-derived, patient-specific recommendations which are available to the physician during the medical decision-making process. 7. A Generalized Portable SHMEM Library for High Performance ComputingKrzysztof Parzyszek
This presentation will describe a portable one-sided communication library GPSHMEM that follows the interfaces of the successful SHMEM library introduced by Cray Research Inc. for their distributed memory systems: the Cray T3D and T3E. The portability is achieved by relying on ARMCI, a low-level communication library developed to support one-sided communication in distributed array libraries and compiler run-time systems, and multiple message passing interfaces, including MPI. The presentation will discuss implementation, requirements, performance and initial experience with GPSHMEM.
8. Location Services and Communications in Pervasive ComputingYing Cai
It is believed that the wireless revolution will have a more impact on our society than today's commercial Internet. In particular, the advance in miniaturized electronic devices will create a wireless society with the ability to provide pervasive services gracefully to the human users. In this talk, we first focus on location services in pervasive computing. In particular, we discuss a novel technique for monitoring mobile objects in user-defined regions. In this environment, a user can monitor a region by submitting a range-monitoring query. Unlike conventional queries, which are based on an instant of the database at some moment in time, range-monitoring queries require continuous update on the query results in real time as mobile objects move in and out of the specified regions. Such queries can last for an extended period of time; and many can be active simultaneously. This calls for new techniques to manage queries as conventional database management systems are intended for managing data only. In the second part of this talk, we look at routing issues in mobile ad-hoc networks. A pervasive computing environment must allow a large number of mobile devices to communicate with each other through the wireless network created by themselves without relying on any fixed network infrastructure. Since the network topology changes constantly, flooding is commonly used to recognize neighboring mobile devices in order to establish the desired communication paths. Existing flooding techniques, however, are very expensive because they incur many unnecessary broadcast retransmissions. To substantially reduce this overhead, we propose a method called Edge Forwarding. This scheme leverages location information to limit the flooding to the boundaries of the broadcast coverage.
9. The Similarity Metric (Distinguished Lecture)Paul Vitanyi
A new class of metrics appropriate for measuring effective similarity relations between sequences, say one type of similarity per metric, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of Kolmogorov complexity, and show that it minorizes every metric in the class (that is, it is universal in that it discovers all effective similarities). We demonstrate that it too is a metric and takes values in [0,1]; hence it may be called the similarity metric . This is a theory foundation for a new general practical tool. We give two distinctive applications in widely divergent areas (the experiments by necessity use just computable approximations to the target notions). First, we computationally compare whole mitochondrial genomes and infer their evolutionary history. This results in a first completely automatic computed whole mitochondrial phylogeny tree. Secondly, we give fully automatically computed language tree of 52 different language based on translated versions of the ``Universal Declaration of Human Rights''.
This is joint work with Ming Li, Xin Chen, Xin Li, Bin Ma, and wil be presented at the 14th ACM-SIAM Symposium on Discrete Algorithms, Baltimore, 2003. It can be accessed at http://www.cwi.nl/~paulv/selection.html
Speaker Biographies
Xiaoqiu HuangXiaoqiu Huang is Associate Professor at ISU's Computer Science Department and the Plant Institute's Laurence H. Baker Center for Bioinformatics and Biological Statistics. He earned his Master's and Doctoral degrees in computer science at Pennsylvania State University. Dr. Huang was on the faculty at Michigan Technological University from 1990 to 1999. Before coming to Iowa State, he was Associate Professor at the Keck Graduate Institute of Life Sciences in Claremont, Calif. and Principal Scientist at Paracel Inc. in Pasadena.
Dr. Huang's research in bioinformatics focuses on three computational problems in genome sequencing and analysis; (1) assembly of DNA fragments into longer sequences, (2)identification of genes in genomic DNA sequences, and (3) comparison of genomic DNA sequences.
Visit Xiaoqiu Huang's hompage here.
Yoonsik CheonYoonsik Cheon is currently a Ph.D. candidate in the Department of Computer Science at Iowa State University. Since 1995, he has been working for Electronics and Telecommunications Research Institute (ETRI) of Korea as a member of technical staff. He holds a MS in Computer Science from Iowa State, and a BS in Computer Science from Korea University. His primary research interest is in formal methods, in particular, practical application of formal specifications into object-oriented programming.
Visit Yoonsik Cheon's hompage here.
Michael Sanderson Michael Sanderson is a Professor of Evolution and Ecology at the University of California, Davis. He earned his B.S from the University of Arizona in Physics and his Ph.D from the University of Arizona in Ecology and Evolutionary Biology. He then served as a Postdoctoral fellow (Sloan Fellowship in Molecular Evolution) at Cornell University. His research interests are in systematics and phylogenetics of flowering plants, theoretical issues in macroevolution, and molecular evolution.Visit Michael Sanderson's hompage here.
Francine D. BermanDr. Francine Berman is Director of the San Diego Supercomputer Center and the National Partnership for Advanced Computational Infrastructure, ACM Fellow, Professor of Computer Science and Engineering at U. C. San Diego, and Director of the UCSD Grid Laboratory. Over the last two decades, her research has focused on the development of software, tools and models for Parallel and more recently Grid Computing environments. Dr. Berman has served on numerous program committees, advisory boards and steering committees and currently serves as one of the two Principal Investigators for NSF's $53,000,000 TeraGrid project.
Visit Francine D. Berman's hompage here.
Alan TribbleDr. Alan Tribble is a principal systems engineer in the Advanced Technology Center at Rockwell Collins in Cedar Rapids, IA. He also teaches courses in Electrical and Computer Engineering at the University of Iowa. Dr. Tribble received his Ph.D. in Physics from the University of Iowa. Currently he is co-PI on a $3M NASA project funded by the Aviation Safety Program. Dr. Tribble has authored numerous technical publications and four books, including The Space Environment - Implications for Spacecraft Design, Princeton Guide to Advanced Physics, Fundamentals of Contamination Control, and A Tribble's Guide to Space.
Visit Alan Tribble's hompage here.
Piet de GroenDr. Piet de Groen is consultant in Gastroenterology and Hepatology at the Mayo Clinic in Rochester, MN. He is an Associate Professor in Medicine and Gastroenterology at Mayo Medical School.
Dr. de Groens clinical research objective is to decrease the mortality due to cholangiocarcinoma (cancer of the bile ducts) by actively pursuing early detection of this disease in patients at risk, develop new or improve current diagnostic modalities, and finally investigate new treatment options. Mayo Clinic Rochester is one of the largest referral centers for this type of tumor.
In addition, Dr. de Groen has an interest in bioinformatics. He has led the development of web-based databases and applications for the Mayo Clinic Cancer Center in Rochester and currently is the Program Director at Mayo Clinic Rochester of the Mayo Clinic/IBM Computational Biology Collaboration which is developing a comprehensive prototype system for access to and interpretation of clinical, genomic as well as proteomic data.
Visit Piet de Groen's hompage here.
Krzysztof ParzyszekKrzysztof Parzyszek is currently a PhD student in Department of Computer Science at Iowa State University. Since January 2000 he has been working as a Research Assistant in the Scalable Computing Laboratory of Ames Laboratory, DoE. In 1999 he obtained a Master's degree in Mathematics from Warsaw University of Technology in Warsaw, Poland. His interests include high performance computing and design and implementation of programming languages.
Visit Krzysztof Parzyszek's hompage here.
Ying CaiYing Cai received his Ph.D. in computer science from the University of Central Florida (UCF) in 2002, and his MS and BS, both in computer science, from Jiaotong University, Xi'an, China, in 1993 and 1990, respectively. His research interests include wireless networks, mobile computing, multimedia communications, storage systems, and database management systems. Dr. Cai has published many papers and made a few significant contributions to these fields. In particular, the paper on Patching techniques, he published in ACM Multimedia'98, has collected more than 50 citations; and "patching" has become a standard term used in the literature today. Early this year, Dr. Cai received the Hillman Award at UCF for his outstanding research work. While studying at this university, Dr. Cai was a director at nStor leading the effort to develop network storage technology. Dr. Cai is currently a project leader at ImageSoft Technologies. Last year, his team delivered the first distributed image archive system for the finance industry. Dr. Ying Cai is a member of IEEE and ACM.
Visit Ying Cai's hompage here.
Paul VitanyiPaul M.B. Vitanyi received his Ph.D. from the Free University of Amsterdam (1978) and he holds positions at the national CWI Research Institute in Amsterdam and is professor of Computer Science at the University of Amsterdam. He serves on the editorial boards of Distributed Computing, Information Processing Letters, Theory of Computing Systems, Parallel Processing Letters, International journal of Foundations of Computer Science, Journal of Computer and Systems Sciences (guest editor), and elsewhere. He has worked on cellular automata, computational complexity, distributed and parallel computing, machine learning and prediction, physics of computation, Kolmogorov complexity, quantum computing. Together with Ming Li they pioneered applications of Kolmogorov complexity and co-authored ``An Introduction to Kolmogorov Complexity and its Applications,'' Springer-Verlag, New York, 1993 (2nd Edition 1997), parts of which have been translated into Chinese, Russian and Japanese. Web page: http://www.cwi.nl/~paulv/
Visit Paul Vitanyi's hompage here.
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Contacts
Thank you for visiting this page. Please send your suggestions and comments to one of us in the Computer Science colloquium committee.
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ananthk@cs.iastate.edu