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2009
ACM
159views Algorithms» more  STOC 2009»
16 years 5 months ago
Message passing algorithms and improved LP decoding
Linear programming decoding for low-density parity check codes (and related domains such as compressed sensing) has received increased attention over recent years because of its p...
Sanjeev Arora, Constantinos Daskalakis, David Steu...
STOC
2009
ACM
136views Algorithms» more  STOC 2009»
16 years 5 months ago
Random walks on polytopes and an affine interior point method for linear programming
Let K be a polytope in Rn defined by m linear inequalities. We give a new Markov Chain algorithm to draw a nearly uniform sample from K. The underlying Markov Chain is the first t...
Ravi Kannan, Hariharan Narayanan
175
Voted
RECOMB
2009
Springer
16 years 5 months ago
Learning Models for Aligning Protein Sequences with Predicted Secondary Structure
Accurately aligning distant protein sequences is notoriously difficult. A recent approach to improving alignment accuracy is to use additional information such as predicted seconda...
Eagu Kim, Travis J. Wheeler, John D. Kececioglu
RECOMB
2009
Springer
16 years 5 months ago
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
Collective behavior involving distally separate regions in a protein is known to widely affect its function. In this paper, we present an online approach to study and characterize ...
Arvind Ramanathan, Pratul K. Agarwal, Maria Kurnik...
149
Voted
RECOMB
2009
Springer
16 years 5 months ago
Storage and Retrieval of Individual Genomes
A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Example...
Gonzalo Navarro, Jouni Sirén, Niko Väl...