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emcee is a Python library implementing a class of affine-invariant ensemble samplers for Markov chain Monte Carlo (MCMC). This package has been widely applied to probabilistic modeling problems in astrophysics where it was originally…

The Information Dynamics Toolkit xl (IDTxl) is a comprehensive software package for efficient inference of networks and their node dynamics from multivariate time series data using information theory. IDTxl provides functionality to…

Bayesian statistical inverse problems are often solved with Markov chain Monte Carlo (MCMC)-type schemes. When the problems are governed by large-scale discrete nonlinear partial differential equations (PDEs), they are computationally…

BLASFEO is a dense linear algebra library providing high-performance implementations of BLAS- and LAPACK-like routines for use in embedded optimization. A key difference with respect to existing high-performance implementations of BLAS is…

Joint models for longitudinal and time-to-event data constitute an attractive modeling framework that has received a lot of interest in the recent years. This paper presents the capabilities of the R package JMbayes for fitting these models…

DerivKit is a Python package for derivative-based statistical inference. It implements stable numerical differentiation and derivative assembly utilities for Fisher-matrix forecasting and higher-order likelihood approximations in scientific…

UltraNest is a general-purpose Bayesian inference package for parameter estimation and model comparison. It allows fitting arbitrary models specified as likelihood functions written in Python, C, C++, Fortran, Julia or R. With a focus on…

Bayesian experimental design (BED) for complex physical systems is often limited by the nested inference required to estimate the expected information gain (EIG) or its gradients. Each outer sample induces a different posterior, creating a…

1. Understanding the mechanisms underlying biological systems, and ultimately, predicting their behaviours in a changing environment requires overcoming the gap between mathematical models and experimental or observational data.…

Despite the success of deep learning for text and image data, tree-based ensemble models are still state-of-the-art for machine learning with heterogeneous tabular data. However, there is a significant need for tabular-specific…

dame-flame is a Python package for performing matching for observational causal inference on datasets containing discrete covariates. This package implements the Dynamic Almost Matching Exactly (DAME) and Fast Large-Scale Almost Matching…

Modern imaging methods rely strongly on Bayesian inference techniques to solve challenging imaging problems. Currently, the predominant Bayesian computation approach is convex optimisation, which scales very efficiently to high dimensional…

In this study, we present a new module built for users interested in a programming language similar to BUGS to fit a Bayesian model based on the piecewise exponential (PE) distribution. The module is an extension to the open-source program…

LibBi is a software package for state-space modelling and Bayesian inference on modern computer hardware, including multi-core central processing units (CPUs), many-core graphics processing units (GPUs) and distributed-memory clusters of…

In image classification tasks, the ability of deep CNNs to deal with complex image data has proven to be unrivalled. However, they require large amounts of labeled training data to reach their full potential. In specialised domains such as…

Bayesian networks (BNs) are widely used for modeling complex systems with uncertainty, yet repositories of pre-built BNs remain limited. This paper introduces bnRep, an open-source R package offering a comprehensive collection of documented…

Bayesian inference provides a methodology for parameter estimation and uncertainty quantification in machine learning and deep learning methods. Variational inference and Markov Chain Monte-Carlo (MCMC) sampling methods are used to…

SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…

The INLA package provides a tool for computationally efficient Bayesian modeling and inference for various widely used models, more formally the class of latent Gaussian models. It is a non-sampling based framework which provides…

Measuring Mutual Information (MI) between high-dimensional, continuous, random variables from observed samples has wide theoretical and practical applications. Recent work, MINE (Belghazi et al. 2018), focused on estimating tight…