Stan (software)
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Stan (software)
Stan is a probabilistic programming language for statistical inference written in C++.Stan Development Team. 2015Stan Modeling Language User's Guide and Reference Manual, Version 2.9.0/ref> The Stan language is used to specify a (Bayesian) statistical model with an imperative program calculating the log probability density function. Stan is licensed under the New BSD License. Stan is named in honour of Stanislaw Ulam, pioneer of the Monte Carlo method. Stan was created by a development team consisting of 34 members that includes Andrew Gelman, Bob Carpenter, Matt Hoffman, and Daniel Lee. Interfaces The Stan language itself can be accessed through several interfaces: * CmdStan – a command-line executable for the shell, * CmdStanR and rstan – R software libraries, * CmdStanPy and PyStan – libraries for the Python programming language, * MatlabStan – integration with the MATLAB numerical computing environment, * Stan.jl – integration with the Julia programming langua ...
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Unix-like
A Unix-like (sometimes referred to as UN*X or *nix) operating system is one that behaves in a manner similar to a Unix system, although not necessarily conforming to or being certified to any version of the Single UNIX Specification. A Unix-like application is one that behaves like the corresponding Unix command or shell. Although there are general philosophies for Unix design, there is no technical standard defining the term, and opinions can differ about the degree to which a particular operating system or application is Unix-like. Some well-known examples of Unix-like operating systems include Linux and BSD. These systems are often used on servers, as well as on personal computers and other devices. Many popular applications, such as the Apache web server and the Bash shell, are also designed to be used on Unix-like systems. One of the key features of Unix-like systems is their ability to support multiple users and processes simultaneously. This allows users to run multipl ...
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Python Programming Language
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC programming language and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ran ...
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Laplace's Method
In mathematics, Laplace's method, named after Pierre-Simon Laplace, is a technique used to approximate integrals of the form :\int_a^b e^ \, dx, where f(x) is a twice-differentiable function, ''M'' is a large number, and the endpoints ''a'' and ''b'' could possibly be infinite. This technique was originally presented in . In Bayesian statistics, Laplace's approximation can refer to either approximating the posterior normalizing constant with Laplace's method or approximating the posterior distribution with a Gaussian centered at the maximum a posteriori estimate. Laplace approximations play a central role in the integrated nested Laplace approximations method for fast approximate Bayesian inference. The idea of Laplace's method Suppose the function f(x) has a unique global maximum at ''x''0. Let M>0 be a constant and consider the following two functions: :\begin g(x) &= Mf(x) \\ h(x) &= e^ \end Note that ''x''0 will be the global maximum of g and h as well. Now observe ...
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Broyden–Fletcher–Goldfarb–Shanno Algorithm
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 (or approximate gradient evaluations) via a generalized secant method. Since the updates of the BFGS curvature matrix do not require matrix inversion, its computational complexity is only \mathcal(n^), compared to \mathcal(n^) in Newton's method. Also in common use is L-BFGS, which is a limited-memory version of BFGS that is particularly suited to problems with very large numbers of variables (e.g., >1000). The BFGS-B variant handles simple box constraints. The algorithm is named after Charles George Broyden, Roger Fletcher, ...
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Limited-memory BFGS
Limited-memory BFGS (L-BFGS or LM-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 f(\mathbf) over unconstrained values of the real-vector \mathbf where f is a differentiable scalar function. Like the original BFGS, L-BFGS uses an estimate of the inverse Hessian matrix to steer its search through variable space, but where BFGS stores a dense n\times n approximation to the inverse Hessian (''n'' being the number of variables in the problem), L-BFGS stores only a few vectors that represent the approximation implicitly. Due to its resulting linear memory requirement, the L-BFGS method is particularly well suited for optimization problems with many variables. Instead of the inverse Hessian H''k'', L-BFGS maintains a history of t ...
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Journal Of Machine Learning Research
The ''Journal of Machine Learning Research'' is a peer-reviewed open access scientific journal covering machine learning. It was established in 2000 and the first editor-in-chief was Leslie Kaelbling. The current editors-in-chief are Francis Bach (Inria) and David Blei (Columbia University). History The journal was established as an open-access alternative to the journal ''Machine Learning''. In 2001, forty editorial board members of ''Machine Learning'' resigned, saying that in the era of the Internet, it was detrimental for researchers to continue publishing their papers in expensive journals with pay-access archives. The open access model employed by the ''Journal of Machine Learning Research'' allows authors to publish articles for free and retain copyright, while archives are freely available online. Print editions of the journal were published by MIT Press until 2004 and by Microtome Publishing thereafter. From its inception, the journal received no revenue from the pr ...
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Hamiltonian Monte Carlo
The Hamiltonian Monte Carlo algorithm (originally known as hybrid Monte Carlo) is a Markov chain Monte Carlo method for obtaining a sequence of random samples which converge to being distributed according to a target probability distribution for which direct sampling is difficult. This sequence can be used to estimate integrals with respect to the target distribution (expected values). Hamiltonian Monte Carlo corresponds to an instance of the Metropolis–Hastings algorithm, with a Hamiltonian dynamics evolution simulated using a time-reversible and volume-preserving numerical integrator (typically the leapfrog integrator) to propose a move to a new point in the state space. Compared to using a Gaussian random walk proposal distribution in the Metropolis–Hastings algorithm, Hamiltonian Monte Carlo reduces the correlation between successive sampled states by proposing moves to distant states which maintain a high probability of acceptance due to the approximate energy conserving ...
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Optimization (mathematics)
Mathematical optimization (alternatively spelled ''optimisation'') or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfields: discrete optimization and continuous optimization. Optimization problems of sorts arise in all quantitative disciplines from computer science and engineering to operations research and economics, and the development of solution methods has been of interest in mathematics for centuries. In the more general approach, an optimization problem consists of maximizing or minimizing a real function by systematically choosing input values from within an allowed set and computing the value of the function. The generalization of optimization theory and techniques to other formulations constitutes a large area of applied mathematics. More generally, optimization includes finding "best available" values of some objective function given a define ...
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Variational Bayesian Methods
Variational Bayesian methods are a family of techniques for approximating intractable integrals arising in Bayesian inference and machine learning. They are typically used in complex statistical models consisting of observed variables (usually termed "data") as well as unknown parameters and latent variables, with various sorts of relationships among the three types of random variables, as might be described by a graphical model. As typical in Bayesian inference, the parameters and latent variables are grouped together as "unobserved variables". Variational Bayesian methods are primarily used for two purposes: #To provide an analytical approximation to the posterior probability of the unobserved variables, in order to do statistical inference over these variables. #To derive a lower bound for the marginal likelihood (sometimes called the ''evidence'') of the observed data (i.e. the marginal probability of the data given the model, with marginalization performed over unobserved v ...
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Markov Chain Monte Carlo
In statistics, Markov chain Monte Carlo (MCMC) methods comprise a class of algorithms for sampling from a probability distribution. By constructing a Markov chain that has the desired distribution as its equilibrium distribution, one can obtain a sample of the desired distribution by recording states from the chain. The more steps that are included, the more closely the distribution of the sample matches the actual desired distribution. Various algorithms exist for constructing chains, including the Metropolis–Hastings algorithm. Application domains MCMC methods are primarily used for calculating numerical approximations of multi-dimensional integrals, for example in Bayesian statistics, computational physics, computational biology and computational linguistics. In Bayesian statistics, the recent development of MCMC methods has made it possible to compute large hierarchical models that require integrations over hundreds to thousands of unknown parameters. In rare even ...
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Forecasting
Forecasting is the process of making predictions based on past and present data. Later these can be compared (resolved) against what happens. For example, a company might estimate their revenue in the next year, then compare it against the actual results. Prediction is a similar but more general term. Forecasting might refer to specific formal statistical methods employing time series, cross-sectional or longitudinal data, or alternatively to less formal judgmental methods or the process of prediction and resolution itself. Usage can vary between areas of application: for example, in hydrology the terms "forecast" and "forecasting" are sometimes reserved for estimates of values at certain specific future times, while the term "prediction" is used for more general estimates, such as the number of times floods will occur over a long period. Risk and uncertainty are central to forecasting and prediction; it is generally considered a good practice to indicate the degree of uncertainty ...
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Time Series
In mathematics, a time series is a series of data points indexed (or listed or graphed) in time order. Most commonly, a time series is a sequence taken at successive equally spaced points in time. Thus it is a sequence of discrete-time data. Examples of time series are heights of ocean tides, counts of sunspots, and the daily closing value of the Dow Jones Industrial Average. A time series is very frequently plotted via a run chart (which is a temporal line chart). Time series are used in statistics, signal processing, pattern recognition, econometrics, mathematical finance, weather forecasting, earthquake prediction, electroencephalography, control engineering, astronomy, communications engineering, and largely in any domain of applied science and engineering which involves temporal measurements. Time series ''analysis'' comprises methods for analyzing time series data in order to extract meaningful statistics and other characteristics of the data. Time series ''forecasting' ...
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