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{"documenter":{"julia_version":"1.9.3","generation_timestamp":"2023-11-14T18:09:30","documenter_version":"1.1.2"}}
{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-11T20:44:19","documenter_version":"1.2.1"}}
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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Alternatives · HiddenMarkovModels.jl</title><meta name="title" content="Alternatives · HiddenMarkovModels.jl"/><meta property="og:title" content="Alternatives · HiddenMarkovModels.jl"/><meta property="twitter:title" content="Alternatives · HiddenMarkovModels.jl"/><meta name="description" content="Documentation for HiddenMarkovModels.jl."/><meta property="og:description" content="Documentation for HiddenMarkovModels.jl."/><meta property="twitter:description" content="Documentation for HiddenMarkovModels.jl."/><meta property="og:url" content="https://gdalle.github.io/HiddenMarkovModels.jl/alternatives/"/><meta property="twitter:url" content="https://gdalle.github.io/HiddenMarkovModels.jl/alternatives/"/><link rel="canonical" href="https://gdalle.github.io/HiddenMarkovModels.jl/alternatives/"/><script data-outdated-warner src="../assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../search_index.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../"><img src="../assets/logo.png" alt="HiddenMarkovModels.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../">HiddenMarkovModels.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../api/">API reference</a></li><li><span class="tocitem">Tutorials</span><ul><li><a class="tocitem" href="../examples/basics/">Basics</a></li><li><a class="tocitem" href="../examples/types/">Types</a></li><li><a class="tocitem" href="../examples/interfaces/">Interfaces</a></li><li><a class="tocitem" href="../examples/autodiff/">Autodiff</a></li><li><a class="tocitem" href="../examples/temporal/">Time dependency</a></li><li><a class="tocitem" href="../examples/controlled/">Control dependency</a></li></ul></li><li><span class="tocitem">Advanced</span><ul><li class="is-active"><a class="tocitem" href>Alternatives</a><ul class="internal"><li><a class="tocitem" href="#Julia"><span>Julia</span></a></li><li><a class="tocitem" href="#Python"><span>Python</span></a></li></ul></li><li><a class="tocitem" href="../debugging/">Debugging</a></li><li><a class="tocitem" href="../formulas/">Formulas</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Advanced</a></li><li class="is-active"><a href>Alternatives</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Alternatives</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/gdalle/HiddenMarkovModels.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/gdalle/HiddenMarkovModels.jl/blob/main/docs/src/alternatives.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Competitors"><a class="docs-heading-anchor" href="#Competitors">Competitors</a><a id="Competitors-1"></a><a class="docs-heading-anchor-permalink" href="#Competitors" title="Permalink"></a></h1><h2 id="Julia"><a class="docs-heading-anchor" href="#Julia">Julia</a><a id="Julia-1"></a><a class="docs-heading-anchor-permalink" href="#Julia" title="Permalink"></a></h2><p>We compare features among the following Julia packages:</p><ul><li>HiddenMarkovModels.jl (abbreviated to HMMs.jl)</li><li><a href="https://github.com/maxmouchet/HMMBase.jl">HMMBase.jl</a></li><li><a href="https://github.com/idiap/HMMGradients.jl">HMMGradients.jl</a></li></ul><p>We discard <a href="https://github.com/FAST-ASR/MarkovModels.jl">MarkovModels.jl</a> because its focus is GPU computation. There are also more generic packages for probabilistic programming, which are able to perform MCMC or variational inference (eg. <a href="https://github.com/TuringLang/Turing.jl">Turing.jl</a>) but we leave those aside.</p><table><tr><th style="text-align: right"></th><th style="text-align: right">HMMs.jl</th><th style="text-align: right">HMMBase.jl</th><th style="text-align: right">HMMGradients.jl</th></tr><tr><td style="text-align: right">Algorithms</td><td style="text-align: right">Sim, FB, Vit, BW</td><td style="text-align: right">Sim, FB, Vit, BW</td><td style="text-align: right">FB</td></tr><tr><td style="text-align: right">Observation types</td><td style="text-align: right">anything</td><td style="text-align: right"><code>Number</code> / <code>Vector</code></td><td style="text-align: right">anything</td></tr><tr><td style="text-align: right">Observation distributions</td><td style="text-align: right">DensityInterface.jl</td><td style="text-align: right">Distributions.jl</td><td style="text-align: right">manual</td></tr><tr><td style="text-align: right">Multiple sequences</td><td style="text-align: right">yes</td><td style="text-align: right">no</td><td style="text-align: right">yes</td></tr><tr><td style="text-align: right">Priors / structures</td><td style="text-align: right">possible</td><td style="text-align: right">no</td><td style="text-align: right">possible</td></tr><tr><td style="text-align: right">Temporal dependency</td><td style="text-align: right">yes</td><td style="text-align: right">no</td><td style="text-align: right">no</td></tr><tr><td style="text-align: right">Control dependency</td><td style="text-align: right">yes</td><td style="text-align: right">no</td><td style="text-align: right">no</td></tr><tr><td style="text-align: right">Number types</td><td style="text-align: right">anything</td><td style="text-align: right"><code>Float64</code></td><td style="text-align: right"><code>AbstractFloat</code></td></tr><tr><td style="text-align: right">Automatic differentiation</td><td style="text-align: right">yes</td><td style="text-align: right">no</td><td style="text-align: right">yes</td></tr><tr><td style="text-align: right">Linear algebra</td><td style="text-align: right">yes</td><td style="text-align: right">yes</td><td style="text-align: right">no</td></tr><tr><td style="text-align: right">Logarithmic probabilities</td><td style="text-align: right">halfway</td><td style="text-align: right">halfway</td><td style="text-align: right">yes</td></tr></table><p>Sim = Simulation, FB = Forward-Backward, Vit = Viterbi, BW = Baum-Welch</p><h2 id="Python"><a class="docs-heading-anchor" href="#Python">Python</a><a id="Python-1"></a><a class="docs-heading-anchor-permalink" href="#Python" title="Permalink"></a></h2><ul><li><a href="https://github.com/hmmlearn/hmmlearn">hmmlearn</a> (based on NumPy)</li><li><a href="https://github.com/jmschrei/pomegranate">pomegrnate</a> (based on PyTorch)</li><li><a href="https://github.com/probml/dynamax">dynamax</a> (based on JAX)</li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../examples/controlled/">« Control dependency</a><a class="docs-footer-nextpage" href="../debugging/">Debugging »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 11 December 2023 20:44">Monday 11 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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