Search Results for "bayesian" - Page 2
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Showing 177 open source projects for "bayesian"
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bogofilter -- Fast Bayesian Spam Filter
Fast Bayesian spam filter along lines suggested by Paul Graham
The bogofilter package implements a fast Bayesian spam filter as suggested by Paul Graham in "A Plan For Spam" <http://www.paulgraham.com/spam.html>. It is written in C. Supported platforms: Linux, FreeBSD, Solaris, OS X, HP-UX, AIX, RISC-OS, ... -
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see
Visualisation toolbox for beautiful and publication-ready figures
see is an R package that serves as the visualization component of the easystats ecosystem, providing plotting utilities to produce publication-ready visualizations of statistical model parameters, diagnostics, predictions, and performance metrics. It works in conjunction with other easystats packages (such as parameters, performance, modelbased, bayestestR, etc.) to convert model outputs or summary objects into visual forms (dot-and-whisker plots, diagnostic plots, residual plots, etc.). It... -
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PyMC3
Probabilistic programming in Python
...Fit your model using gradient-based MCMC algorithms like NUTS, using ADVI for fast approximate inference — including minibatch-ADVI for scaling to large datasets, or using Gaussian processes to build Bayesian nonparametric models. PyMC3 includes a comprehensive set of pre-defined statistical distributions that can be used as model building blocks. Sometimes an unknown parameter or variable in a model is not a scalar value or a fixed-length vector, but a function. A Gaussian process (GP) can be used as a prior probability distribution whose support is over the space of continuous functions. ... -
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awesome-single-cell
Community-curated list of software packages and data resources
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc. List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Rapid, accurate and memory-frugal preprocessing of single-cell and single-nucleus RNA-seq data. Find bimodal, unimodal, and multimodal features in your data. Ascend is an R package comprised of fast, streamlined analysis functions optimized to... -
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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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RASP
RASP (Reconstruct Ancestral State in Phylogenies)
RASP (Reconstruct Ancestral State in Phylogenies) is a tool for inferring ancestral state using S-DIVA (Statistical dispersal-vicariance analysis), Lagrange (DEC), Bayes-Lagrange (S-DEC), BayArea, BBM (Bayesian Binary MCMC) method, Bayestraits and BioGeoBEARS packages. All documentation and source code for RASP is freely available at: http://mnh.scu.edu.cn/soft/blog/RASP and http://github.com/sculab/RASP -
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pomegranate
Fast, flexible and easy to use probabilistic modelling in Python
...The modular implementation allows one to easily drop normal distributions into a mixture model to create a Gaussian mixture model just as easily as dropping a gamma and a Poisson distribution into a mixture model to create a heterogeneous mixture. But that's not all! Because each model is treated as a probability distribution, Bayesian networks can be dropped into a mixture just as easily as a normal distribution, and hidden Markov models can be dropped into Bayes classifiers to make a classifier over sequences. Together, these two design choices enable a flexibility not seen in any other probabilistic modeling package. -
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Anti-Spam SMTP Proxy Server
Anti-Spam SMTP Proxy Server implements multiple spam filters
The Anti-Spam SMTP Proxy (ASSP) Server project aims to create an open source platform-independent SMTP Proxy server which implements auto-whitelists, self learning Hidden-Markov-Model and/or Bayesian, Greylisting, DNSBL, DNSWL, URIBL, SPF, SRS, Backscatter, Virus scanning, attachment blocking, Senderbase and multiple other filter methods. Click 'Files' to download the professional version 2.8.1 build 24261. A linux(ubuntu 20.04 LTS) and a freeBSD 12.2 based ready to run OVA of ASSP V2 are also available for download. NOTICE: V1 development has been stopped at the end of 2014 (1.10.1 build 16060). ... -
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Bayes+Estimate is a Rust and C++ library that implement numerical algorithms for Bayesian estimation. They provide tested and consistent numerical methods and represents the wide variety of Bayesian estimation algorithms and system model.
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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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BACE for gretl
Bayesian Averaging of Classical Estimates
Bayesian Averaging of Classical Estimates package. -
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Pyro
Deep universal probabilistic programming with Python and PyTorch
Pyro is a flexible, universal probabilistic programming language (PPL) built on PyTorch. It allows for expressive deep probabilistic modeling, combining the best of modern deep learning and Bayesian modeling. Pyro is centered on four main principles: Universal, Scalable, Minimal and Flexible. Pyro is universal in that it can represent any computable probability distribution. It scales easily to large datasets with minimal overhead, and has a small yet powerful core of composable abstractions that make it both agile and maintainable. ... -
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STK
a Small (Matlab/Octave) Toolbox for Kriging
...Its primary focus in on the interpolation / regression technique known as kriging, which is very closely related to Splines and Radial Basis Functions, and can be interpreted as a non-parametric Bayesian method using a Gaussian Process (GP) prior. The STK also provides tools for the sequential and non-sequential design of experiments. Even though it is, currently, mostly geared towards the Design and Analysis of Computer Experiments (DACE), the STK can be useful for other applications areas (such as Geostatistics, Machine Learning, Non-parametric Regression, etc.). -
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R packages (maintained by YJLEE)
R packages for PK/PD modeling , BE/BA, drug stability, ivivc, etc.
These R packages are developed for data analysis of PK/PD modeling & simulation, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM). -
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Statistical Rethinking 2024
This course teaches data analysis
...It provides updated notebooks, R scripts, and model examples, some streamlined and restructured compared to previous years. The 2024 repo also highlights the transition toward more robust Stan models and integration with newer Bayesian workflow practices, continuing to emphasize accessibility for learners while modernizing the tools. This version is designed for students following the 2024 lecture series, offering the most current set of examples, exercises, and teaching material aligned with the Statistical Rethinking framework. Online, flipped instruction. I will pre-record the lectures each week. ... -
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Bayesian Julia
Bayesian Statistics using Julia and Turing
Bayesian statistics incorporate uncertainty (and prior knowledge) by allowing probability statements about parameters. -
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BMA for gretl
Bayesian Model Averaging
Bayesian Model Averaging package -
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Habfuzz
A command-line tool for data-driven fuzzy modelling
Input 1 - A training dataset (multiple observations) of up to four variables (predictors) against one (response variable) Input 2 - A test dataset (multiple observations) of the same four variables with unknown response variable Output - Calculation of the response variable for each test observation using fuzzy logic or fuzzy rule-based Bayesian algorithms HABFUZZ is a habitat model, which can be used in ecohydraulic modelling applications for the calculation of the instream habitat suitability in various discharge scenarios in a simulated river reach. It comes with no graphical user interface but it's a one-click tool. Just provide your input and let HABFUZZ provide you the output. ... -
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Neural Tangents
Fast and Easy Infinite Neural Networks in Python
Neural Tangents is a high-level neural network API for specifying complex, hierarchical models at both finite and infinite width, built in Python on top of JAX and XLA. It lets researchers define architectures from familiar building blocks—convolutions, pooling, residual connections, and nonlinearities—and obtain not only the finite network but also the corresponding Gaussian Process (GP) kernel of its infinite-width limit. With a single specification, you can compute NNGP and NTK kernels,... -
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Statistical Rethinking 2023
Statistical Rethinking Course for Jan-Mar 2023
...It continues to provide scripts for lectures and tutorials, while integrating refinements to examples, notation, and computational workflows introduced that year. Compared with 2022, some models are rewritten for clarity, and teaching materials reflect refinements in McElreath’s evolving presentation of Bayesian data analysis. Students following the 2023 lecture videos use this repository as their coding reference. There are 10 weeks of instruction. Links to lecture recordings will appear in this table. Weekly problem sets are assigned on Fridays and due the next Friday, when we discuss the solutions in the weekly online meeting. -
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pattern_classification
A collection of tutorials and examples for solving machine learning
...It includes notebooks and guides that demonstrate data preprocessing, feature extraction, model training, and evaluation techniques used in machine learning workflows. The repository also covers algorithms such as Bayesian classification, logistic regression, neural networks, clustering methods, and ensemble models. In addition to algorithm tutorials, the project contains supplementary resources such as dataset collections, visualization examples, and links to recommended books and talks. These materials are designed to support both theoretical understanding and practical experimentation with machine learning tools. -
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pexm - JAGS module
JAGS module for the piecewise exponential distribution
This new module was built for users interested in a programming language similar to BUGS to fit a Bayesian model based on the piecewise exponential distribution. The module is an extension of the open-source program JAGS. The PE distribution is widely used in the fields of survival analysis and reliability. Currently, it can only be implemented in JAGS through methods to indirectly specify the likelihood based on the Poisson or Bernoulli probabilities. -
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...Citation: 1. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 Aug;73(16):5261-7. 2. Wang Q, Cole JR. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc. 2024 Apr 11;13(4):e0106323.
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CausalNex
A Python library that helps data scientists to infer causation
CausalNex is a Python library that uses Bayesian Networks to combine machine learning and domain expertise for causal reasoning. You can use CausalNex to uncover structural relationships in your data, learn complex distributions, and observe the effect of potential interventions. -
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Bayesian Methods for Hackers
An introduction to Bayesian methods + probabilistic programming
Bayesian Methods for Hackers is the source repository for Bayesian Methods for Hackers, an educational book about Bayesian inference and probabilistic programming. It is written from a computation-first perspective, prioritizing intuition, examples, and executable notebooks over heavy mathematical formalism. The project introduces readers to uncertainty, Bayesian modeling, MCMC, priors, posteriors, and real-world probabilistic reasoning.