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BMCBI
2010
109views more  BMCBI 2010»
13 years 3 months ago
Free energy estimation of short DNA duplex hybridizations
Background: Estimation of DNA duplex hybridization free energy is widely used for predicting cross-hybridizations in DNA computing and microarray experiments. A number of software...
Dan C. Tulpan, Mirela Andronescu, Serge Leger
NIPS
2000
13 years 5 months ago
Generalized Belief Propagation
In an important recent paper, Yedidia, Freeman, and Weiss [11] showed that there is a close connection between the belief propagation algorithm for probabilistic inference and the...
Jonathan S. Yedidia, William T. Freeman, Yair Weis...
NIPS
2001
13 years 5 months ago
TAP Gibbs Free Energy, Belief Propagation and Sparsity
The adaptive TAP Gibbs free energy for a general densely connected probabilistic model with quadratic interactions and arbritary single site constraints is derived. We show how a ...
Lehel Csató, Manfred Opper, Ole Winther
NIPS
2004
13 years 5 months ago
Expectation Consistent Free Energies for Approximate Inference
We propose a novel a framework for deriving approximations for intractable probabilistic models. This framework is based on a free energy (negative log marginal likelihood) and ca...
Manfred Opper, Ole Winther
BIOCOMP
2006
13 years 5 months ago
Melting Free Energies of DNA Duplexes with oxidized Base Residues and Abasic sites: A Molecular Dynamics Characterization
: Ionizing radiation alters DNA strands and mainly creates multiply damaged sites (MDS), e.g. two or more damaged sites within one or two turns of the DNA (10 to 20 base pairs). Th...
Latifa Douali, Matt Ernst, John Miller, Michel Dup...
BIOCOMP
2006
13 years 5 months ago
An Approach to Selecting Putative RNA Motifs Using MDL Principle
The history of molecular biology is punctuated by a series of discoveries demonstrating the surprising breadth of biological roles of ribonucleic acid (RNA). An ensemble of evoluti...
Mohammad Anwar, Marcel Turcotte
UAI
2008
13 years 5 months ago
Convergent Message-Passing Algorithms for Inference over General Graphs with Convex Free Energies
Inference problems in graphical models can be represented as a constrained optimization of a free energy function. It is known that when the Bethe free energy is used, the fixedpo...
Tamir Hazan, Amnon Shashua
STOC
2010
ACM
220views Algorithms» more  STOC 2010»
13 years 7 months ago
Combinatorial approach to the interpolation method and scaling limits in sparse random graphs
We establish the existence of free energy limits for several sparse random hypergraph models corresponding to certain combinatorial models on Erd¨os-R´enyi graph G(N, c/N) and r...
Mohsen Bayati, David Gamarnik, Prasad Tetali
ICASSP
2008
IEEE
13 years 10 months ago
Using variational bayes free energy for unsupervised voice activity detection
This paper addresses the problem of Voice Active Detection (VAD) in noisy environments. We introduce Variational Bayes approach to EM for classification to replace the heuristic ...
David Cournapeau, Tatsuya Kawahara
RECOMB
2006
Springer
14 years 4 months ago
RNA Secondary Structure Prediction Via Energy Density Minimization
Abstract. There is a resurgence of interest in RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery of many new families of non-coding R...
Can Alkan, Emre Karakoç, Süleyman Cenk...