[Colloquium] Reminder: Guest Speakers at TTI-C June 5-9, 2006

[Katherine Cumming]

**********TTI-C Guest Speakers Next Week***********
			June 5 - June 9
Presented by:  Toyota Technological Institute at Chicago


(1) 
Speaker:  Robert Kleinberg,  University of California, Berkeley
Speaker's home page:  http://theory.lcs.mit.edu/~rdk/


Date: Monday, June 5, 2006
Location: TTI-C Conference Room
Time:  11:00am


Title:   Learning an Admission Threshold
 

Abstract:

 We will present algorithms for a class of online learning problems in which
the function to be learned satisfies a monotonicity constraint.  A
prototypical example is the following problem.  Suppose you are presented
with a list of n tests, whose success probabilities form a monotonically
increasing sequence.  Other than this monotonicity property, you have no
knowledge of the success probabilities of the tests.  You must perform a
sequence of experiments, each consisting of choosing one of the n tests and
observing the outcome of a Bernoulli trial with the corresponding success
probability.  The goal is to identify the test which is closest to having a
specified success probability, using as few experiments as possible.  (This
can be regarded as a binary search problem with noisy feedback.)  We present
algorithms which match the information-theoretic lower bound, up to a
constant factor, for this problem and some related search problems.
    This is joint work with Richard Karp.
 
(2)
Speaker:  Sean Mooney, Indiana University
Speaker's Homepage:  http://compbio.iupui.edu/mooney/

Date:  Monday, June 5, 2006
Location:  TTI-C Conference Room
Time:  2:00pm

Title:  Tools for Annotation of Sequence and Structurally Conserved
Environments in Proteins


Abstract:

As a relatively new discipline, bioinformatics continues to grow and mature.
Over the past two years my laboratory has focused on the important
bioinformatic problem of building computational models of protein function
from experimentally determined three dimensional structure. To this end, we
have developed a website, http://www.sblest.org, and a suite of web
services, that enables users to submit protein structures and identify the
sequence and structurally conserved environments in that query. To do this,
we integrated several sequence and structure based analysis tools, such as
S-BLEST, PSI-BLAST, and HMMer to identify sites that are associated with
SCOP families, GO terms and EC terms. In addition to the website, we have
built a suite of web services for accessing this resource, and have extended
UCSF Chimera and Delano Scientific PyMOL to use this. Overall, this method
enables researchers to identify structurally conserved sites. We have also
begun to evaluate the attributes derived from this method by using them as
input to classify catalytic residues in proteins. We have then ranked these
features based on their ability to classify. This approach has enabled us to
evaluate our method and suggests that methods such as this have a bright
future for finding and characterizing functional elements. 



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If you have questions, or would like to meet the speaker, please contact
Katherine at 773-834-1994 or kcumming at tti-c.org   For information on future
TTI-C talks and events, please go to the TTI-C Events page:
http://www.tti-c.org/events.html.  TTI-C (1427 East 60th Street, Chicago, IL
60637)