Please join the eScience Institute on Monday, September 30, 4:00 pm in
EEB-303. Refreshments will be provided.
*Orly Alter (Utah):*
Orly Alter, Ph.D. is a USTAR Associate Professor of Bioengineering and
Human Genetics at the Scientific Computing and Imaging (SCI) Institute at
the University of Utah. She was awarded a National Science Foundation
CAREER Award in 2009, and a National Human Genome Research Institute
(NHGRI) R01 grant in 2007. She was selected to give the Linear Algebra and
its Applications Lecture of the International Linear Algebra Society in
2005, and received an NHGRI Individual Mentored Research Scientist
Development Award in Genomic Research and Analysis in 2000, and a Sloan
Foundation/Department of Energy Postdoctoral Fellowship in Computational
Molecular Biology in 1999. Additional support for her work comes from the
Utah Science, Technology and Research (USTAR) Initiative.
Discovery of Principles of Nature from Matrix and Tensor Modeling of
Large-Scale Molecular Biological Data
In my Genomic Signal Processing Lab, we are breaking new ground in
mathematics, at the interface of mathematics, biology and medicine, and in
biology and medicine. In mathematics, we develop generalizations of the
mathematical frameworks that underlie the theoretical description of the
physical world [1]. At the interface, we use these frameworks to create
models that compare and integrate different types of large-scale molecular
biological data. In biology and medicine, we use the models to
computationally predict previously unknown physical, cellular and
evolutionary mechanisms that govern the activity of DNA and RNA. We
believe that future discovery and control in biology and medicine will come
from the mathematical modeling of large-scale molecular biological data,
just as Kepler discovered the laws of planetary motion by using mathematics
to describe trends in astronomical data [2].
At the interface, our recent generalized singular value decomposition
(GSVD) comparison of two patient-matched genomic datasets uncovered a
global pattern of DNA aberrations that is correlated with, and possibly
causally related to, brain cancer survival [3]. This new link between a
glioblastoma multiforme (GBM) tumor’s genome and a patient’s prognosis
offers insights into the cancer’s formation and growth, and suggests
promising drug targets. The best prognostic predictor of GBM prior to this
discovery was the patient’s age at diagnosis. In mathematics, the
higher-order GSVD we formulated is the only framework to date that enables
comparison of more than two patient-matched but probe-independent datasets,
and, in general, more than two datasets arranged in matrices of the same
column dimensions but different row dimensions [4]. In biology, our
experiments [5] verified our prediction [6] of a global causal coordination
between DNA replication origin activity and mRNA expression, demonstrating
that matrix and tensor modeling of DNA microarray data [7] can be used to
correctly predict previously unknown biological modes of regulation.
Ultimately we hope to bring physicians a step closer to one day being able
to predict and control the progression of cell division and cancer as
readily as NASA engineers plot the trajectories of spacecraft today.
Friday, September 20, 2013
FLAS Fellowships for undergraduate, graduate and professional students
Foreign
Language & Area Studies Fellowships (FLAS) available to undergraduate,
graduate and professional
students
Receive tuition and a
living stipend:
Academic Year
Graduate:
$18,000 tuition, $15,000 living
stipend
Academic Year Undergraduate:
$10,000 tuition, $5,000 living
stipend
Summer
Graduate/Undergraduate: $5,000
tuition, $2,500 living stipend
The FLAS
Fellowship is available to
U.S. citizens and permanent residents. FLAS
Fellowships support study of the following languages and their world
regions:
-Arabic –Bangla
-Bosnian/Croatian/Serbian –Bulgarian –Burmese -Canadian First Nations –Chinese
–Czech –Danish -Estonian -Filipino/Tagalog –Finnish –French –German –Hebrew
–Hindi -Indonesian/Malay –Italian –Japanese –Kazakh –Khmer –Korean –Latvian
–Lithuanian –Norwegian –Persian –Polish –Portuguese –Russian –Slovenian –Spanish
–Swahili –Swedish –Tajik –Thai –Turkish –Uighur –Urdu –Uzbek
–Vietnamese
FLAS
Information Sessions,
covering FLAS benefits and requirements, the application process, and the use of
FLAS awards abroad, will be held at the following dates and times:
-
Undergraduate Fellowship Fair, Oct 10, 10-2,Mary Gates Hall, FLAS Session 11:30-12:20 MGH 206
-
Study Abroad Fair, Wed, Oct 23, 10-2, Mary Gates Hall, FLAS Session 10:30-11 MGH 258
-
Thomson 317: T Oct 29, 3:30-4:30/ Wed Nov 6, 2:30-3:30/ T Nov 26, 2:30-3:30
-
Denny 213: Wed Nov 13, 3:30-4:30
-
UW Bothell 1-103, Nov 14, 3:30-5
-
Parrington 313: Wed Dec 4, 2:30-3:30Applications due January 15, 2014. Questions: email flas@uw.edu
Thursday, September 19, 2013
Welcome Back! Forum on Science, Ethics, and Policy (FOSEP) Student Group
Welcome back new and continuing students, staff, and faculty to the
University of Washington!
Science affects nearly every aspect of American policy. Several major challenges faced by society have solutions that are based on science, yet there is little emphasis to educate scientists in training about policy and communication. To improve the impression of science in culture and the support of scientific research among taxpayers and policy makers, scientists must engage in effective communication and participate in policy discussions.
The *Forum on Science, Ethics, and Policy (FOSEP)* at the University of Washington is a group of dedicated undergraduate, graduate, and post-doctoral fellows who are concerned about a range of issues that surround the practice and funding of research. We believe FOSEP can successfully educate its student members about the intersection of science and society in a way that is not accessible within a traditional graduate education. With this mission, FOSEP is training the citizen scientists of the future.
*More information* regarding FOSEP can be found at: http://seattlefosep.wordpress.com/
*If interested in joining* FOSEP, please complete this short (very short) catalyst survey at https://catalyst.uw.edu/webq/survey/ragatsum/212834. Responsibilities of general FOSEP members are negligible, but we do hope that you will attend FOSEP events and spread the word about FOSEP in your department.
*Please join us on October 8th at 5pm for an introduction to FOSEP * and a lively discussion of the way scientific research, and specifically health information, is communicated. We will be looking at conflicting reports about the health effects of caffeine. With conflicting reports seemingly presented every week by scientists, does the public gain or lose trust in science as an institution? Refreshments will be provided. Please *RSVP to leaders@fosep.org*.
Science affects nearly every aspect of American policy. Several major challenges faced by society have solutions that are based on science, yet there is little emphasis to educate scientists in training about policy and communication. To improve the impression of science in culture and the support of scientific research among taxpayers and policy makers, scientists must engage in effective communication and participate in policy discussions.
The *Forum on Science, Ethics, and Policy (FOSEP)* at the University of Washington is a group of dedicated undergraduate, graduate, and post-doctoral fellows who are concerned about a range of issues that surround the practice and funding of research. We believe FOSEP can successfully educate its student members about the intersection of science and society in a way that is not accessible within a traditional graduate education. With this mission, FOSEP is training the citizen scientists of the future.
*More information* regarding FOSEP can be found at: http://seattlefosep.wordpress.com/
*If interested in joining* FOSEP, please complete this short (very short) catalyst survey at https://catalyst.uw.edu/webq/survey/ragatsum/212834. Responsibilities of general FOSEP members are negligible, but we do hope that you will attend FOSEP events and spread the word about FOSEP in your department.
*Please join us on October 8th at 5pm for an introduction to FOSEP * and a lively discussion of the way scientific research, and specifically health information, is communicated. We will be looking at conflicting reports about the health effects of caffeine. With conflicting reports seemingly presented every week by scientists, does the public gain or lose trust in science as an institution? Refreshments will be provided. Please *RSVP to leaders@fosep.org*.
Space Available in CSE 467 for EE Majors
We will have 5 spaces open for EE majors who want to take 467 this fall. The prerequisites for them will be : EE 271 and EE 478.
CSE467: Advanced Digital Design – Gabriel Cohn
How you ever wondered how the Xbox Kinect and other computer vision systems can compute complicated algorithms on large data sets in real-time? Take CSE 467 to learn how to dramatically accelerate an algorithm by implementing it on custom hardware! Such hardware acceleration is commonly used for high speed computations in computer vision, artificial intelligence, computational biology, and finance. The class project will allow students to implement a highly optimized computer vision algorithm on an FGPA.
Wednesday, September 18, 2013
Undergraduate Research Opportunities in EE
I am looking to hire hourly
student research assistants for the fall
quarter for three
different projects.
1) Automatic speech recognition for low-resource languages: Current speech recognition technology relies on machine learning methods that leverage large amounts of transcribed data. In this project, we are interested in languages other than English, in which case there may not be a lot of data available. This project will involve harvesting data from the web for augmenting small data sets and learning methods that account for style differences.
2) Automatic detection and classification of marine mammals: Detection of marine mammals is important for avoiding sonar operations when they are present and for tracking populations. The problem is challenging because of the highly variable noise conditions in the oceans. We have developed some prototype algorithms in Matlab and are looking for someone to work on porting these algorithms to C/C++ and factoring the implementation to leverage parallel processing and allow experimentation with large amounts of data. Once the software is in place, the goal is to explore semi-supervised learning algorithms.
3) Speaking style analysis: Spoken language carries much more information than one can see in the transcript, including emotion, strength of belief, sarcasm, etc. In this project, we investigate signal processing methods to extract cues that an automatic system could use to recognize this information.
All projects will require computer implementation of algorithms for data processing and analysis.
1) Automatic speech recognition for low-resource languages: Current speech recognition technology relies on machine learning methods that leverage large amounts of transcribed data. In this project, we are interested in languages other than English, in which case there may not be a lot of data available. This project will involve harvesting data from the web for augmenting small data sets and learning methods that account for style differences.
2) Automatic detection and classification of marine mammals: Detection of marine mammals is important for avoiding sonar operations when they are present and for tracking populations. The problem is challenging because of the highly variable noise conditions in the oceans. We have developed some prototype algorithms in Matlab and are looking for someone to work on porting these algorithms to C/C++ and factoring the implementation to leverage parallel processing and allow experimentation with large amounts of data. Once the software is in place, the goal is to explore semi-supervised learning algorithms.
3) Speaking style analysis: Spoken language carries much more information than one can see in the transcript, including emotion, strength of belief, sarcasm, etc. In this project, we investigate signal processing methods to extract cues that an automatic system could use to recognize this information.
All projects will require computer implementation of algorithms for data processing and analysis.
Qualification/expertise:
Computer programming skills and
experience, including: experience with unix,
programming languages such as C, C++ or Java and
scripting languages such as Perl or Python.
Students should have completed and done well in
both CS142 and 143 (at least). Knowledge of
probability is very useful for anticipated work
on machine learning. For projects 2 & 3,
experience with Matlab is desirable.
Hours & Salary:
The position will
involve 10-19 hrs/week, flexible hours, depending
on student availability. The salary is $12-15/hr,
depending on experience.
Application Documents:
CV,
(unofficial) transcript, and the contact
information of one or two references,
including either the instructor for one of
your programming courses or a supervisor for
whom you've done programming.
Contact:
Interested candidates may
send their application material to Prof.
Ostendorf at ostendor@u.washington.edu.
If you are interested in the first position,
please copy Aaron Jaech (ajaech@uw.edu),
if interested in the second position, please
copy Nicole Nichols (nmn3@u.washington.edu),
and if interested in the third position, please
copy Vicky Zayats (vzayats@uw.edu).
Tuesday, September 17, 2013
RFID Programming Short-Term Job
Currently we get our RFID tags that we use on some supplies that we
provide to school districts from China. The RFID tags use the ISO 156393
IC- Code SLI protocol. I do have the information that gets written into
the RFID blocks (which are subsequently locked) and the other blocks
are left unwritten, the machines that use our supplies write code on it.
I have some equipment here at our Warehouse in Renton. It should not
take more than 2 hours of your time. I am willing to pay $100/hr. I can
give you pictures and more information of the tags once you find a
proper candidate. The tags use NPX chips.
Let me know.
Francis S Whelan
Witt Company
800-777-0852
850 SW 7th Street Suite 100
Renton, WA 98057
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