Search Results for "bayesian" - Page 2
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Showing 58 open source projects for "bayesian"
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FamSeq
Variant calling on the basis of pedigree information
...FamSeq accommodates de novo mutations and can perform variant calling at chromosome X. To accommodate variations in data complexity, FamSeq consists of three distinct 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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phcfM
R package for modelling anthropogenic deforestation
...It was named after the REDD+ pilot-project 'programme holistique de conservation des forêts à Madagascar'. phcfM includes two main functions: (i) demography(), to model the population growth with time in a hierarchical Bayesian framework using population census data and Gaussian linear mixed models and (ii) deforestation(), to model the deforestation process in a hierarchical Bayesian framework using land-cover change data and Binomial logistic regression models with variable time-intervals between land-cover observations. The two functions use embedded Gibbs samplers written in C++ with the Scythe statistical library to reduce computational time. -
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msBayes allows complex and flexible phylogeographic inference. More specifically, you can test the simultaneous divergence (TSD) of multiple population (species) pairs. It uses approximate Bayesian computation (ABC) under a hierarchical model.
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fesslix
Stochastic Analysis
A brief summary of the main features of Fesslix: - Perform non-intrusive reliability analysis or Bayesian updating either --- by running commands on the command line or --- by means of an Octave interface or --- by means of a Python interface - Flexible input language for writing Fesslix parameter files --- Control flow statements (e.g. if, for, while) --- Most parameters can be defined as functions - Working with response surfaces - Linear finite element analysis using truss, beam and plane stress/strain elements - Spectral Stochastic Finite Elements - Bayesian networks This is the download page for Windows executables of Fesslix. -
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MCTIMME
Microbial Counts Trajectories Infinite Mixture Model Engine
MCTIMME is a nonparametric Bayesian computational framework for analyzing microbial time-series data.The current implementation is in Matlab. -
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abc-sde
approximate Bayesian computation for stochastic differential equations
A MATLAB toolbox for approximate Bayesian computation (ABC) in stochastic differential equation models. It performs approximate Bayesian computation for stochastic models having latent dynamics defined by stochastic differential equations (SDEs) and not limited to the "state-space" modelling framework. Both one- and multi-dimensional SDE systems are supported and partially observed systems are easily accommodated. -
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Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).
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Provide a reference implementation of Moving Taylor Bayesian Regression, a method for nonparametric multi-dimensional function estimation with correlated errors from finite samples, as a Python package based on SciPy
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ABC-DynF
Adaptive Bayesian Classifier with Dynamic Features
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AdPreqFr4SL
Adaptive Prequential Learning Framework
The AdPreqFr4SL learning framework for Bayesian Network Classifiers is designed to handle the cost / performance trade-off and cope with concept drift. Our strategy for incorporating new data is based on bias management and gradual adaptation. Starting with the simple Naive Bayes, we scale up the complexity by gradually updating attributes and structure. Since updating the structure is a costly task, we use new data to primarily adapt the parameters and only if this is really necessary, do we adapt the structure. ... -
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Bayesloc
Bayesian Hierarchical Seismic Event Locator
Given a set of seismic arrivals for one or more events, Bayesloc estimates the joint probability of event locations, corrections to travel time predictions, precision of arrival time measurements, and phase labels for the arrival times. Bayesloc also accepts probabilistic prior constraints on any of the input parameters, which can significantly tighten the distribution of all parameters. -
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The Automated Parameter Estimation and Model Selection Toolkit is a fast, parallelized MCMC engine written in C for Bayesian inference (parameter estimation and model selection).
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Open Bayes is a python free/open library that allows users to easily create a bayesian network and perform inference/learning on it. It is mainly inspired from the Bayes Net Toolbox (BNT) but uses python as a base language. www.openbayes.org
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Feedisto is your personal newspaper. Your newspaper is collocted from rss feeds, parsed by a bayesian filter to rate its relevance and served as a static html page or on a webserver to train the filter. Writing plugins is very easy.
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BASILISK is a probabilistic model of the conformational space of amino acid side chains in proteins. Unlike rotamer libraries, BASILISK models the chi angles in continuous space, including the influence of the protein's backbone.
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DANGLE: A Bayesian inferential prediction method for protein backbone dihedral angles and secondary structure assignments, solely from sequence information, experimental chemical shifts and a database of known protein structures and their shifts.
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This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.
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JBendge - Bayesian Estimation of Nonlinear Dynamic General Equilibrium Models. The project provides a toolkit together with a graphical user interface for the specification, solution, estimation and simulation of models.
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Projeny (Probablistic Networks Generator in Java) is a graphical (Java SWT) front-end to BNT (Bayes Net Toolbox for Matlab). Projeny requires BNT, JMatLink and a Matlab back-end. There is no installable release package, but source code is available on SVN - please check out from SVN to use Projeny. Projeny was started with BNJ as the base.
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Bayesian Surprise Matlab toolkit is a basic toolkit for computing Bayesian surprise values given a large set of input samples. It is also useful as way of exploring surprise theory. For more information see also: http://ilab.usc.edu/
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The application Crimeblips provides up-to-date crime statistics for Berlin (Germany). It maps and visualizes crimes, allowing users to identify crime hot spots, trends and general patterns. Bayesian algorithms are used to extract relevant information.
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software for identifying modules in networks (e.g. "community detection"), as described in "a bayesian approach to network modularity" (physical review letters 100, 258701 (2008); http://link.aps.org/abstract/PRL/v100/e258701).
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A C++ library for Bayesian computation, including a collection of more generally-applicable utilities.
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