A hidden Markov model (HMM) is a Markov model in which the observations are dependent on a latent Markov process. An HMM requires that there be an observable process whose outcomes depend on the outcomes of in a known way. Since cannot be observed directly, the goal is to learn about state of by observing . By definition of being a Markov model, an HMM has an additional requirement that the outcome of at time must be "influenced" exclusively by the outcome of at and that the outcomes of and at must be conditionally independent of at given at time . Estimation of the parameters in an HMM can be performed using maximum likelihood estimation. For linear chain HMMs, the Baum–Welch algorithm can be used to estimate parameters.
A Bayesian network is a probabilistic graphical model that represents a set of variables and their conditional dependencies via a directed acyclic graph (DAG). While it is one of several forms of causal notation, causal networks are special cases of Bayesian networks. Bayesian networks are ideal for taking an event that occurred and predicting the likelihood that any one of several possible known causes was the contributing factor. For example, a Bayesian network could represent the probabilistic relationships between diseases and symptoms. Given symptoms, the network can be used to compute the probabilities of the presence of various diseases.
In statistics, Markov chain Monte Carlo (MCMC) is a class of algorithms used to draw samples from a probability distribution. Given a probability distribution, one can construct a Markov chain whose elements' distribution approximates it – that is, the Markov chain's equilibrium distribution matches the target distribution. The more steps that are included, the more closely the distribution of the sample matches the actual desired distribution.
Bayesian statistics is a theory in the field of statistics based on the Bayesian interpretation of probability, where probability expresses a degree of belief in an event. The degree of belief may be based on prior knowledge about the event, such as the results of previous experiments, or on personal beliefs about the event. This differs from a number of other interpretations of probability, such as the frequentist interpretation, which views probability as the limit of the relative frequency of an event after many trials. More concretely, analysis in Bayesian methods codifies prior knowledge in the form of a prior distribution.
In numerical optimization, the Broyden–Fletcher–Goldfarb–Shanno (BFGS) algorithm is an iterative method for solving unconstrained nonlinear optimization problems. Like the related Davidon–Fletcher–Powell method, BFGS determines the descent direction by preconditioning the gradient with curvature information. It does so by gradually improving an approximation to the Hessian matrix of the loss function, obtained only from gradient evaluations via a generalized secant method.
Conditional random fields (CRFs) are a class of statistical modeling methods often applied in pattern recognition and machine learning and used for structured prediction. Whereas a classifier predicts a label for a single sample without considering "neighbouring" samples, a CRF can take context into account. To do so, the predictions are modelled as a graphical model, which represents the presence of dependencies between the predictions. What kind of graph is used depends on the application. For example, in natural language processing, "linear chain" CRFs are popular, for which each prediction is dependent only on its immediate neighbours. In image processing, the graph typically connects locations to nearby and/or similar locations to enforce that they receive similar predictions.
Limited-memory BFGS is an optimization algorithm in the family of quasi-Newton methods that approximates the Broyden–Fletcher–Goldfarb–Shanno algorithm (BFGS) using a limited amount of computer memory. It is a popular algorithm for parameter estimation in machine learning. The algorithm's target problem is to minimize over unconstrained values of the real-vector where is a differentiable scalar function.
GNU MCSim is a suite of simulation software. It allows one to design one's own statistical or simulation models, perform Monte Carlo simulations, and Bayesian inference through (tempered) Markov chain Monte Carlo simulations. The latest version allows parallel computing of Monte Carlo or MCMC simulations.
Probabilistic programming (PP) is a programming paradigm in which probabilistic models are specified and inference for these models is performed automatically. It represents an attempt to unify probabilistic modeling and traditional general purpose programming in order to make the former easier and more widely applicable. It can be used to create systems that help make decisions in the face of uncertainty.
The Hamiltonian Monte Carlo algorithm is a Markov chain Monte Carlo method for obtaining a sequence of random samples whose distribution converges to a target probability distribution that is difficult to sample directly. This sequence can be used to estimate integrals of the target distribution, such as expected values and moments.
Bayesian inference using Gibbs sampling (BUGS) is a statistical software for performing Bayesian inference using Markov chain Monte Carlo (MCMC) methods. It was developed by David Spiegelhalter at the Medical Research Council Biostatistics Unit in Cambridge in 1989 and released as free software in 1991.
LaplacesDemon is an open-source statistical package that is intended to provide a complete environment for Bayesian inference. LaplacesDemon has been used in numerous fields. The user writes their own model specification function and selects a numerical approximation algorithm to update their Bayesian model. Some numerical approximation families of algorithms include Laplace's method, numerical integration, Markov chain Monte Carlo (MCMC), and variational Bayesian methods.
PyMC is a probabilistic programming language written in Python. It can be used for Bayesian statistical modeling and probabilistic machine learning.
The following outline is provided as an overview of, and topical guide to, machine learning:
Stochastic gradient Langevin dynamics (SGLD) is an optimization and sampling technique composed of characteristics from Stochastic gradient descent, a Robbins–Monro optimization algorithm, and Langevin dynamics, a mathematical extension of molecular dynamics models. Like stochastic gradient descent, SGLD is an iterative optimization algorithm which uses minibatching to create a stochastic gradient estimator, as used in SGD to optimize a differentiable objective function. Unlike traditional SGD, SGLD can be used for Bayesian learning as a sampling method. SGLD may be viewed as Langevin dynamics applied to posterior distributions, but the key difference is that the likelihood gradient terms are minibatched, like in SGD. SGLD, like Langevin dynamics, produces samples from a posterior distribution of parameters based on available data. First described by Welling and Teh in 2011, the method has applications in many contexts which require optimization, and is most notably applied in machine learning problems.
Richard McElreath is an American professor of anthropology and a director of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. He is an author of the Statistical Rethinking applied Bayesian statistics textbook, among the first to largely rely on the Stan statistical environment, and the accompanying rethinking R language package.
ArviZ is a Python package for exploratory analysis of Bayesian models. It is specifically designed to work with the output of probabilistic programming libraries like PyMC, Stan, and others by providing a set of tools for summarizing and visualizing the results of Bayesian inference in a convenient and informative way. ArviZ also provides a common data structure for manipulating and storing data commonly arising in Bayesian analysis, like posterior samples or observed data.
Probabilistic numerics is an active field of study at the intersection of applied mathematics, statistics, and machine learning centering on the concept of uncertainty in computation. In probabilistic numerics, tasks in numerical analysis such as finding numerical solutions for integration, linear algebra, optimization and simulation and differential equations are seen as problems of statistical, probabilistic, or Bayesian inference.
In probability theory and Bayesian statistics, the Lewandowski-Kurowicka-Joe distribution, often referred to as the LKJ distribution, is a probability distribution over positive definite symmetric matrices with unit diagonals.
Bambi is a high-level Bayesian model-building interface written in Python. It works with the PyMC probabilistic programming framework. Bambi provides an interface to build and solve Bayesian generalized (non-)linear multivariate multilevel models.
