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Series: Other Talks

A discussion of the paper "Algorithm independent properties of RNA secondary structure predictions" by Tacker et all (1996).

Series: Other Talks

Host: Carlos Sa de Melo, School of Physics

How advances in science are made, and how they may come to benefit mankind at large are complex issues. The
discoveries that most infuence the way we think about nature seldom can be anticipated, and frequently the
applications for new technologies developed to probe a specific characteristic of nature are also seldom clear,
even to the inventors of these technologies. One thing is most clear: seldom do individuals make such advances
alone. Rather, they result from the progress of the scientific community, asking questions, developing new
technologies to answer those questions, and sharing their results and their ideas with others. However, there are
indeed research strategies that can substantially increase the probability of one's making a discovery, and the
speaker will illustrate some of these strategies in the context of a number of well known discoveries, including the
work he did as a graduate student, for which he shared the Nobel Prize for Physics in 1996.

Series: Other Talks

The goal in matrix recovery problems is to estimate an unknown rank-r
matrix S of size m based on a set of n observations. It is easy to see
that even in the case where the observations are not contaminated with
noise, there exist low rank matrices that cannot be recovered based on n
observations unless n is very large. In order to deal with these cases,
Candes and Tao introduced the called low-coherence assumptions and a
parameter \nu measuring how low-coherent the objective matrix S is.
Using the low-coherence assumptions, Gross proved that S can be recovered
with high probability if n>O(\nu r m \log^2(m)) by an estimator based on
nuclear norm penalization. Let's consider the generalization of the matrix
recovery problem where the matrix S is not only low-rank but also "smooth"
with respect to the geometry given by a graph G. In this 40 minutes long
talk, the speaker will present an approximation error bound for a proposed
estimator in this generalization of the matrix recovery problem.

Series: Other Talks

A discussion of the paper "Linear trees and RNA secondary structure" by Schmitt and Waterman (1994) and, as time permits, "Combinatorics of RNA secondary structures" by Hofacker, Schuster, and Stadler (1998).

Series: Other Talks

A discussion of the papers "RNA folding at elementary step resolution" by Flamm et al (2000) and "Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme" by Isambert and Siggia (2000).

Series: Other Talks

A discussion of the paper "Beyond energy minimization: approaches to the kinetic folding of RNA'' by Flamm and Hofacker (2008).

Series: Other Talks

A discussion of the paper "Evidence for kinetic effects in the folding of large RNA molecules" by Morgan and Higgs (1996).

Series: Other Talks

A discussion of the paper "Using Motion Planning to Study RNA Folding Kinetics" by Tang et al (J Comp Biol, 2005).

Series: Other Talks

Further discussion of alternative metrics on RNA secondary structures.

Series: Other Talks

Alternative metrics on RNA secondary structures will be presented and discussed.