Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling [PDF]
Nature Communications, 2023 Relative binding free energy calculations have become an integral computational tool for lead optimization in structure-based drug design. Classical alchemical methods, including free energy perturbation or thermodynamic integration, compute relative ...
Michael T. Robo +4 more
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High-frequency spike inference with particle Gibbs sampling [PDF]
eLifeCalcium-sensitive fluorescent indicators enable monitoring of spiking activity in large neuronal populations in animal models. Despite the plethora of algorithms developed over the past decades, accurate spike-time inference methods for spike rates ...
Giovanni Diana +4 more
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Bayesian Estimation of the DINA Model With Pólya-Gamma Gibbs Sampling [PDF]
Frontiers in Psychology, 2020 With the increasing demanding for precision of test feedback, cognitive diagnosis models have attracted more and more attention to fine classify students whether has mastered some skills.
Zhaoyuan Zhang +3 more
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Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks [PDF]
BMC Genomics, 2016 Background Phylogenetic networks are leaf-labeled graphs used to model and display complex evolutionary relationships that do not fit a single tree. There are two classes of phylogenetic networks: Data-display networks and evolutionary networks.
Yun Yu +2 more
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Computational phase transition signature in Gibbs sampling
Journal of Physics: Complexity, 2023 Gibbs sampling is fundamental to a wide range of computer algorithms. Such algorithms are set to be replaced by physics based processors—be it quantum or stochastic annealing devices—which embed problem instances and evolve a physical system into a low ...
Hariphan Philathong +3 more
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PhyloGibbs-MP: module prediction and discriminative motif-finding by Gibbs sampling. [PDF]
PLoS Computational Biology, 2008 PhyloGibbs, our recent Gibbs-sampling motif-finder, takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space. Here,
Rahul Siddharthan
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Performance of Alternative BVAR Models for Forecasting Iranian Macroeconomic Variables: An Application of Gibbs Sampling [PDF]
فصلنامه پژوهشهای اقتصادی ایران, 2015 Low and stable inflation with sustainable growth is the first objective of any monetary authority. To achieve this prime goal, reliable forecast of macroeconomic variables play an important role.
Hassan Heidari, Parisa Jouhari Salmasi
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Gibbs state preparation for commuting Hamiltonian: Mapping to classical Gibbs sampling [PDF]
QuantumGibbs state preparation, or Gibbs sampling, is a key computational technique extensively used in physics, statistics, and other scientific fields. Recent efforts for designing fast mixing Gibbs samplers for quantum Hamiltonians have largely focused on ...
Yeongwoo Hwang, Jiaqing Jiang
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Gibbs-Slice Sampling Algorithm for Estimating the Four-Parameter Logistic Model
Frontiers in Psychology, 2020 The four-parameter logistic (4PL) model has recently attracted much interest in educational testing and psychological measurement. This paper develops a new Gibbs-slice sampling algorithm for estimating the 4PL model parameters in a fully Bayesian ...
Jiwei Zhang +5 more
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A Dirichlet Process Prior Approach for Covariate Selection
Entropy, 2020 The variable selection problem in general, and specifically for the ordinary linear regression model, is considered in the setup in which the number of covariates is large enough to prevent the exploration of all possible models.
Stefano Cabras
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