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December
ICSI has signed a memo-of-understanding (MOU) with the China Scholarship Council to create a new international visitors' program--"Chinese Scholars
at ICSI" (CSI). The CSI program will bring up to ten young and upcoming Chinese scientists to ICSI each year, and will emphasize collaborative research initiatives with sponsoring commercial partners. The new call for applicants to ICSI's Spanish visitor program has been announced. The current call (in Spanish) is available here. October
ICSI's Eran Halperin and UCSD's Eleazar Eskin have analysed the genetic data in the National Institute of Health's dbSNP database of the National Center for Biotechnology Information (NCBI), using HAP, the haplotype analysis software they developed. The total size of the dataset analyzed is more than double that of previous datasets.
HAP has been used successfully to perform genetic analysis on large datasets (see Science, Feb. 18, 2005), but modifications were needed for the algorithms to work with the dbSNP data, which includes all publicly available data on single nucleotide polymorphisms (SNPs). SNPs are locations in the human DNA sequence where variation occurs in a population. The HAP program was adapted to be able to handle the different types and sources of data in the dbSNP database, and extended to analyze mother, father and child trios, to provide further genetic information.
HAP analyzed the SNPs in more than 286 million haplotypes for this study, capturing the majority of genetic variation in the dataset. This was accomplished in under 24 hours.
The results of the dbSNP analysis appear in a special issue of Genome Research, published on October 26. Eskin and Halperin hope that the scientific community will use the data they have made available as tools in their genetic research. The duo is designing disease association studies that make use of their data as well as the HAP tool. Nelson Morgan, Eran Halperin, and Vern Paxson formed an ICSI delegation to
Finland the week of October 10, visiting a number of key institutions
including HIIT, HUT, VTT, TUT, the Turku Science Park, Tekes, Nokia, SSH,
and F-Secure. The overall goal was to initiate potential collaborations,
particularly for the Berkeley-Finland visitor program, and to participate in
technical exchanges with Finnish scientists in the areas of speech
processing, bioinformatics, and internet research. The talks were quite
productive, and we expect to be seeing a number of new Finnish researchers
visiting ICSI in the coming year as a direct result of these events. September
Jaron Lanier was named by Foreign Policy and Prospect magazines as one of the
top 100 public intellectuals, defined by the FP website as "someone who has shown distinction in their own field along with the ability to communicate ideas and influence debate outside of it". Foreign Policy invited the public to vote for their top five from this list of 100. Voting has now closed, but the list can be seen here. Results of the poll will be made public in November. ICSI's annual Board of Trustees meeting took place on September 30th. New board member, Dr. Jouko Salo, was elected to replace Dr. Ilpo Reitmaa. Reitmaa has been named Technology Counselor for the Finnish Liaison for the European Union in Brussels.
Dr. Salo has been affiliated with ICSI for several years through TEKES and the Finnish visitor program, and was unanimously approved by the trustees to succeed Dr. Reitmaa. ICSI's Research Review was expanded this year to an all day event. The review, held on September 29th, included talks on exciting research topics at ICSI, as well as demonstrations of newly developed technology. Members of ICSI's Board of Trustees, as well as ICSI research partners and current staff were in attendance to learn more about the varied research topics at ICSI. Featured topics included worm forensics, question answering systems, speaker recognition, machine learning algorithms, extreme computer architecture, CoPE, FrameNet, a hybrid model for human blood clotting, and haplotype resolution software (HAP). August
An article about Richard Karp, head of the
Algorithms Group, appeared in the August-October 2005 issue of the
French journal Les
Dossiers de la Recherche. Author Claire Kenyon, a
professor at Brown University, discusses Karp's contributions in the area NP complete problems, which is the work he is most well known for,
but adds, "there are few areas in computer science
where he has not made an important contribution."
A second article in the journal, entitled "What is P=NP" discusses Karp's
contributions to demonstrating the significance of the P=NP problem which, roughly speaking, asks whether all the combinatorial problems in a very large class called NP can be solved by
efficient algorithms.
One of Karp's contributions in this area was showing that
21 problems well-known problems are NP-complete, which implies that,
if any one of them can be solved efficiently, then all the problems in NP
can be solved efficiently. July
FrameNet Release 1.2 is now available for licensing. FrameNet is a
semantically rich, machine-readable lexicon of English and a corresponding
set of annotated sentences for use in advanced natural language processing
(NLP) applications.
FrameNet draws on more than two decades of research into the semantics of
natural language by Charles Fillmore of ICSI and the University of
California at Berkeley. "Professor Fillmore's theory of Frame Semantics
provides a way to recognize when different words and expressions are being
used to describe the same concept," said Collin Baker, FrameNet project
manager. "Humans instantly understand that 'Mary sold John that book for
$20 dollars' and 'John bought that book from Mary for $20' are two ways of
expressing the same basic idea, but to develop NLP applications like
question answering and machine translation you need a formal, computational
representation of this fact; that's what FrameNet provides."
FrameNet Website >>
June
Scott Shenker, head of the Networking Group and Vice President of ICSI, has been selected to receive the 2006 IEEE Internet Award, for contributions toward an understanding of resource sharing on the Internet. This award is presented annually for exceptional contributions to the advancement of Internet technology for network architecture, mobility and/or end-use applications. Sally Floyd of the Networking Group received the 2005 award. Clarissa, a voice-enabled procedure browser developed by NASA Ames, ICSI, UCSC and Xerox Research Center Europe, was successfully tested for the first time on the International Space Station on June 27th by astronaut John Phillips. To the best of our knowledge, this is the first ever use of a spoken dialogue system in space. During the test, Phillips completed the interactive Clarissa training procedure, which exercises all the main system functionality. ICSI's Manny Rayner worked on the development of Clarissa and is thrilled that it is now working in space.
Clarissa home page on NASA's website.
Summary of system performance during the June 27 ISS test
ICSI technical report on spoken language processing in Clarissa
Article in New Scientist
Article on discovery.com
Members of ICSI's Speech Group recently participated in the Rich
Transcription Spring'05 evaluation, RT-05S, sponsored by the
National Institute of Standards and Technology (NIST).
This annual
evaluation targets the automatic processing of audio recordings from
meetings, establishing benchmarks in core recognition capabilities.
ICSI submitted systems for both the speech transcription task (or "Speech-to-text") and the speaker segmentation and tracking task ("Speaker Diarization"), and peformed very well in both categories.
The creation of these systems was a team effort in collaboration with SRI International.
Official results will be made publicly
available by NIST at the upcoming MLMI'05 (Machine Learning and Multimodal Interaction) conference in Edinburgh in July. Professor Wen Gao of the Chinese Academy of Sciences has been named ICSI's newest External Fellow. Professor Gao was recently described in IEEE Spectrum as one of "Ten to Watch" among China's leading technologists. He heads a China-led international group developing a royalty-free video standard called AVS. He will be working with us to develop China-ICSI collaborations. Congratulations to Mary and Martin Penilla! Their second child, a baby boy, was born on Wednesday, June 2nd at 9:30 pm. He was five pounds nine ounces at birth and nineteen inches long. Research on the Witty worm by Vern Paxson, Nick Weaver, and Abhishek Kumar continued to make headlines in June. After the write-up by Robert Lemos appeared online in late May, the research was highlighted on CNET news.com, ZDnet, monstersandcritics.com, New Scientist magazine and P2Pnet.net. Following the Science write-up of color naming research by Terry Regier, Paul Kay, and Richard Cook, several publications including New Scientist magazine and The Guardian published summaries of the results of the study. ICSI's Paul Kay is known for his work on color naming with Brent Berlin. The new study with Terry Regier builds on his prior research about color naming universals and shows that strong universal tendencies in color naming exist in languages of both industrialized and non-industrialized societies. May
The Proceedings of the National Academy of Sciences published a paper on color naming worldwide by Terry Regier, a frequent ICSI visitor, Paul Kay, a senior researcher in ICSI's AI Group, and Richard Cook, an ICSI postdoctoral resarcher. On May 23, 2005, a write-up about this research appeared on Science Magazine's online daily news site, sciencenow.com, in an article called "Carving Up the Rainbow". A paper analyzing the Witty worm by ICSI security experts Vern Paxson and Nick Weaver, along with former ICSI intern Abhishek Kumar, was the focus of an article by Robert Lemos on Security Focus online on May 24, 2005. A recent study co-authored by Dr. Eran Halperin of ICSI with scientists at Perlegen and UC San Diego was reviewed in MIT's Technology Review magazine. The project, the first of three studies featured in "From The Lab: Biotech" by Monya Baker in the June, 2005 issue, is described as a "gene map shortcut" which uses a subset of SNPs to describe human genetic variation. Read the Article >> Professor Dan Klein of the UC Berkeley Computer Science Faculty is ICSI's newest Faculty Associate. Professor Klein's area of expertise is natural language processing, and he will be affiliated with the Speech Group.
ICSI's speaker recognition group, a subset of the Speech Group, participated in the 2005 speaker
recognition evaluation conducted by the National Institute of
Standards and Technology (NIST). These evaluations are an important
contribution to the calibration of technical capabilities and are of
interest to researchers working on the general problem of
text-independent speaker recognition worldwide.
ICSI's submitted system was one of the top performers in the core test condition. The
effort was led by staff scientist Nikki Mirghafori and showcased work of
students Kofi Boakye, Dan Gillick, Andy Hatch, and Steve Stafford, with
important contributions from SRI's Speaker Recognition team. Congratulations to Dr. Barry Chen who received his Ph.D. in Electrical Engineering from UC Berkeley in May, 2005. While working toward his doctorate, Barry was also a graduate student researcher with ICSI's Speech Group. Congratulations, Dr. Chen. Nicholas Weaver, network security expert at ICSI was quoted in an article on worm attacks on instant messaging in New Scientist. The article appears on page 26 of the May 14, 2005 issue, and is also available online here >> April
Eric Fosler-Lussier has been named an ICSI External Fellow. He is a Professor in the Computer Science and Engineering department at Ohio State University. Fosler-Lussier is a former graduate student researcher and postdoctoral researcher with ICSI's Speech Group, and as an External Fellow will collaborate with ICSI on speech projects. ICSI cybersecurity research by Vern Paxson and Nicholas Weaver of the Networking Group is featured in an article on Creative Match, a UK search engine featuring user submitted content. Read the article >> Professor Shankar Sastry, Chairman of the ICSI Board of Trustees and a Professor of Electrical Engineering and Computer Science at UC Berkeley, has been named the new director of the UC Berkeley-based Center for Information Technology Research in the Interest of Society (CITRIS). Full Story >> March
The FrameNet Project has a new website. The redesigned site features news and information about FrameNet as well as a forum and a new tool, FrameGrapher, which allows users to browse the frame relations graphically. FrameNet Website >> Professor Richard M. Karp of ICSI's Algorithms Group will
be speaking at the Institute for Systems Biology's Fourth International
Symposium in Seattle, Washington in April. More
information on the Symposium >>
Karp is also an invited speaker at the 2nd Brazilian Symposium
on Graphs, Algorithms and Combinatorics (GRACO 2005), also in April, in
Rio de Janeiro, Brazil. The
GRACO 2005 website >> February
On Friday, February 18, Science published the study
"Whole-Genome Patterns of Common DNA Variation in Three Human
Populations." The collaborative study by researchers at Perlegen
Sciences, ICSI, and Calit2, developed a map of the human genome which is
expected to be a major medical tool in fighting genetic diseases. More >> The American Association for the Advancement
of Science released an article entitled "Map of human genetic
variation across populations may promise improved disease
treatments" on Thursday, February 17. The article is available online from the AAAS newsroom. Dr. Eran Halperin of ICSI's
Algorithms group is a co-author of the featured study and is one of the
developers of HAP, the haplotyping software used in the study. Professor Richard M. Karp, head of the ICSI Algorithms
Group, and Roded Sharan, a former postdoc at ICSI, participated in a
study comparing DNA of baker's yeast, a worm, and fruit flies, which was
published in the Proceedings of the National Academy of Sciences
on February 8. Karp and Sharan collaborated with researchers from UCSD
and the Institute of Genetics in Karlsruhe, Germany on this study. More information from the UCSD News website.
The ICSI Open House is on Thursday, February
10 from 2:00-4:00 p.m. This year's event includes an introduction to the
Institute, a feature presentation on XORP: eXtensible Open-source Router
Platform, and demonstrations of the following technological developments
at ICSI: Rapid Speech Prototyping: The Tamil Recognizer, The ICSI
Meeting Project, HAP: Haplotype Resolution using Imperfect Phylogeny,
FrameNet, and CoPe: Community of Practice Environment. Researchers at ICSI develop speech
recognition technology for India. A demonstration of this technology
will be presented at the ICSI Open House on Thursday, February 10th.
Read the press release.
>> January
Srini Narayanan, leader of ICSI's AI group, started a new
position as Adjunct Professor of Cognitive Science at UC Berkeley in
January. -
On January 17, 2005, the Spanish Ministry for
Education and Science posted the 2005 call for proposals for ICSI's
Spanish Visitor Program. This program provides support for postdoctoral
scholars from Spain to participate in research visits to ICSI. Spanish
researchers interested in applying to the program, please visit the MEC website. >>
-
A new version of HAP, a software program
designed to aid in identification of genetic factors in human disease,
will be released in early 2005. Eran Halperin and Richard Karp of ICSI,
and Eleazar Eskin of UC San Diego, developed this software, which has so
far aided hundreds of researchers worldwide in decoding more than 4000
sets of genetic data. More information on HAP is available at the HAP
information page as well as a recent article from the website of the California
Institute for Telecommunications and Information Technology.
-
CLARISSA, a spoken dialogue system to be used
by astronauts, was delivered to the International Space Station by a
Russian rocket on December 25, 2004. ICSI researcher Manny Rayner worked
with NASA's Beth Ann Hockey to develop the system, which will read
procedures to astronauts and can also answer simple questions, take
notes, and display pictures. For more information on CLARISSA, see the
NASA article. >>
-
Jaron Lanier, an inventor, musician and
researcher affiliated with ICSI, was featured in an article in The
Register on December 27th, 2004. He discusses his views on technology,
religion and metaphysics with reporter Andrew Orlowski in the article. >>
-
Dr. Eran Halperin, a former post-doc with Dr.
Richard M. Karp of the Algorithms Group, returned to ICSI in January to
be a full time research scientist. Dr. Halperin will be focusing on
bioinformatics, a field that utilizes computational algorithms in
biological research. He is particularly interested in genetics,
haplotypes and disease association.
-
Dr. Yang Liu, a researcher in ICSI's Speech
Group, received her Ph.D. in Electrical and Computer Engineering from
Purdue University on December 19, 2004. Dr. Liu's thesis,
"Structural Event Detection for Rich Transcription of Speech"
was defended on December 3rd to committee members Mary Harper, Elizabeth
Shriberg (also of ICSI's Speech Group), Leah Jamieson and Jack Gandour.
Her thesis research was conducted at ICSI as part of the DARPA EARS
program. Congratulations Dr. Liu!
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The ICSI Gazette
September 2005 (pdf)
March 2005 (pdf)
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