Search Results for "markov chain monte carlo"
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Showing 19 open source projects for "markov chain monte carlo"
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MonteCarlo.jl
Classical and quantum Monte Carlo simulations in Julia
MonteCarlo.jl is a package implementing classical and quantum Monte Carlo simulations primarily for solid state physics. Currently the focus is on finding a overall design for the package and verifying that determinant Quantum Monte Carlo (DQMC) is working correctly. As such the package may still go through significant changes and the documentation may be outdated and incomplete. Note that classical Monte Carlo is also not a focus at this point. It is probably usable, but a lot... -
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TensorFlow Probability
Probabilistic reasoning and statistical analysis in TensorFlow
... using a single language throughout the lifecycle of model exploration and production. TFP is open source and available on GitHub. Tools to build deep probabilistic models, including probabilistic layers and a `JointDistribution` abstraction. Variational inference and Markov chain Monte Carlo. A wide selection of probability distributions and bijectors. Optimizers such as Nelder-Mead, BFGS, and SGLD. -
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Bayesian Statistics
This repository holds slides and code for a full Bayesian statistics
This repository holds slides and code for a full Bayesian statistics graduate course. Bayesian statistics is an approach to inferential statistics based on Bayes' theorem, where available knowledge about parameters in a statistical model is updated with the information in observed data. The background knowledge is expressed as a prior distribution and combined with observational data in the form of a likelihood function to determine the posterior distribution. The posterior can also be used... -
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Gen.jl
A general-purpose probabilistic programming system
An open-source stack for generative modeling and probabilistic inference. Gen’s inference library gives users building blocks for writing efficient probabilistic inference algorithms that are tailored to their models, while automating the tricky math and the low-level implementation details. Gen helps users write hybrid algorithms that combine neural networks, variational inference, sequential Monte Carlo samplers, and Markov chain Monte Carlo. Gen features an easy-to-use modeling language... -
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JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
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UnBBayes
Framework & GUI for Bayes Nets and other probabilistic models.
UnBBayes is a probabilistic network framework written in Java. It has both a GUI and an API with inference, sampling, learning and evaluation. It supports Bayesian networks, influence diagrams, MSBN, OOBN, HBN, MEBN/PR-OWL, PRM, structure, parameter and incremental learning. Please, visit our wiki (https://sourceforge.net/p/unbbayes/wiki/Home/) for more information. Check out the license section (https://sourceforge.net/p/unbbayes/wiki/License/) for our licensing policy. -
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CAMPARI
Software for molecular simulations and trajectory analysis
... and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. CAMPARI offers the user a very high level of control over all implemented features. For more information and features, please refer to the project's homepage at http://campari.sourceforge.net/V5 -
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Bridge.jl
A statistical toolbox for diffusion processes
Statistics and stochastic calculus for Markov processes in continuous time, include univariate and multivariate stochastic processes such as stochastic differential equations or diffusions (SDE's) or Levy processes. -
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Muninn
A software package for estimating generalized ensemble weights in Mark
We have moved to GitHub: https://github.com/muninnorg/muninn As of July 2015 we have moved to GitHub. The SourceForge page will preserved, with the old releases. Muninn is a software package for estimating generalized ensemble weights in Markov chain Monte Carlo (MCMC) simulations. The method is full automated and makes use of the generalized multihistogram (GMH) equations for estimation the density of states [1]. The package is implemented in C++ and has a convenient interface. -
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StatAlign
An extendable statistical multiple alignment tool.
StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny... -
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MSL
http://dx.doi.org/10.1002/jcc.22968
MSL is a C++ library that enables the computational study of macromolecules. The MSL library is not a program (although some applications are distributed) but a tool for scientist to code their own molecular modeling methods. Philosophy The main goal is to create a set of tools that enable the computational study of macromolecules with relative ease at all levels, from simple operations (for example, load a PDB and measure a distance or edit a dihedral) to complex applications... -
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FamSeq
Variant calling on the basis of pedigree information
... implementations of the Mendelian genetic model: the Bayesian network algorithm, Elston-Stewart algorithm and Markov chain Monte Carlo algorithm. To make the software efficient and applicable to large families, we parallelized the Bayesian network algorithm that copes with pedigrees with inbreeding loops without losing calculation precision on an NVIDIA® graphics processing unit. -
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Hrothgar Parallel LM/MCMC Minimizer
A versatile MCMC and downhill optimization engine
Hrothgar is a parallel minimizer and Markov Chain Monte Carlo generator by Andisheh Mahdavi of San Francisco State University. It has been used to solve optimization problems in astrophysics (galaxy cluster mass profiles) as well as in experimental particle physics (hadronic tau decays). It is probably adaptable enough to be applied to your merit function if you can write it in C. -
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HYDRA is an open-source, platform-neutral library for performing Markov Chain Monte Carlo. It implements the logic of standard MCMC samplers within a framework designed to be easy to use and to extend while allowing integration with other software to
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...: Synthesis-Decompostion Reaction Chain Reaction Nuclear Chemical Reaction Lodka Model Brusselator Model Furthermore, the Stochastic approach can be computed by several stochastic simulation algorithms. The DetStoch package offers four stochastic algorithms that use probability functions simulated via Monte Carlo methods: Gillespie's Direct Method, Gillespie's First Reaction Method, Bruck and Gibson Next Reaction Method and Tau-Leaping Method.
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Matlab toolbox for Markov Chain Monte Carlo. Includes interfaces for storing and retrieving trace and run information.
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NullAllEst is the implementation of a maximum likelihood algorithm to estimate the frequency of a null allele in microsatellite genetic data. A Markov Chain Monte Carlo simulation is used to solve the likelihood function.
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Two Markov-Chain-Monte-Carlo-algorithms ("Glauber Dynamics" and "Flip Dynamics") used for randomly sampling k-colorings of a graph.
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