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    » Self-Organization by Optimizing Free-Energy
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    BIBE
    2007
    IEEE
    138views Bioinformatics» more  BIBE 2007»
    A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots
    15 years 3 months ago
    A Flexible Stem-Based Local Search Algorithm for Predicting RNA Secondary Structures Including Pseudoknots
    Download  www.jdl.ac.cn
    -We demonstrate a new algorithm named FlexStem to predict RNA secondary structures with pseudoknots. Our approach is based on the free energy minimization criterion, and utilizes a...
    Xiang Chen, Simin He, Dongbo Bu, Runsheng Chen, We...
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    UAI
    2003
    172views Artificial Intelligence» more  UAI 2003»
    On the Convergence of Bound Optimization Algorithms
    14 years 10 months ago
    On the Convergence of Bound Optimization Algorithms
    Download  cs.nyu.edu
    Many practitioners who use EM and related algorithms complain that they are sometimes slow. When does this happen, and what can be done about it? In this paper, we study the gener...
    Ruslan Salakhutdinov, Sam T. Roweis, Zoubin Ghahra...
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    UAI
    2004
    148views Artificial Intelligence» more  UAI 2004»
    On the Choice of Regions for Generalized Belief Propagation
    14 years 11 months ago
    On the Choice of Regions for Generalized Belief Propagation
    Download  www.ics.uci.edu
    Generalized belief propagation (GBP) has proven to be a promising technique for approximate inference tasks in AI and machine learning. However, the choice of a good set of cluste...
    Max Welling
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    JCC
    2006
    82views more  JCC 2006»
    Monte Carlo simulations of biomolecules: The MC module in CHARMM
    14 years 9 months ago
    Monte Carlo simulations of biomolecules: The MC module in CHARMM
    Download  dinner-group.uchicago.edu
    : We describe the implementation of a general and flexible Monte Carlo (MC) module for the program CHARMM, which is used widely for modeling biomolecular systems with empirical ene...
    Jie Hu, Ao Ma, Aaron R. Dinner
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    GECCO
    2006
    Springer
    154views Optimization» more  GECCO 2006»
    Emergent mating topologies in spatially structured genetic algorithms
    15 years 1 months ago
    Emergent mating topologies in spatially structured genetic algorithms
    Download  www.cs.bham.ac.uk
    The application of network analysis to emergent mating topologies in spatially structured genetic algorithms is presented in this preliminary study as a framework for inferring ev...
    Joshua L. Payne, Margaret J. Eppstein
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