/usr/share/doc/python-pebl/html/prior.html is in python-pebl-doc 1.0.2-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>prior – Prior models — Pebl v1.0.1 documentation</title>
<link rel="stylesheet" href="_static/default.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '',
VERSION: '1.0.1',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
};
</script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="top" title="Pebl v1.0.1 documentation" href="index.html" />
<link rel="up" title="API Reference" href="apiref.html" />
<link rel="next" title="result – Learner results" href="result.html" />
<link rel="prev" title="posterior – Posterior distribution" href="posterior.html" />
</head>
<body>
<div class="related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
<a href="result.html" title="result – Learner results"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="posterior.html" title="posterior – Posterior distribution"
accesskey="P">previous</a> |</li>
<li><a href="index.html">Pebl v1.0.1 documentation</a> »</li>
<li><a href="apiref.html" accesskey="U">API Reference</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body">
<div class="section" id="module-pebl.prior">
<span id="prior-prior-models"></span><h1><tt class="xref py py-mod docutils literal"><span class="pre">prior</span></tt> – Prior models<a class="headerlink" href="#module-pebl.prior" title="Permalink to this headline">¶</a></h1>
<p>This module provides classes for representing and working with prior models.</p>
<dl class="class">
<dt id="pebl.prior.Prior">
<em class="property">class </em><tt class="descclassname">pebl.prior.</tt><tt class="descname">Prior</tt><big>(</big><em>num_nodes</em>, <em>energy_matrix=None</em>, <em>required_edges=</em><span class="optional">[</span><span class="optional">]</span>, <em>prohibited_edges=</em><span class="optional">[</span><span class="optional">]</span>, <em>constraints=</em><span class="optional">[</span><span class="optional">]</span>, <em>weight=1.0</em><big>)</big><a class="headerlink" href="#pebl.prior.Prior" title="Permalink to this definition">¶</a></dt>
<dd><p>Class for representing prior model.</p>
<blockquote>
<div><dl class="docutils">
<dt>Priors have two aspects: </dt>
<dd><ul class="first last simple">
<li>soft priors: weights for each possible edge.</li>
<li>hard priors: constraints that MUST be met.</li>
</ul>
</dd>
</dl>
<p>Soft priors are specified by an energy matrix, a weight matrix taking
values over [0,1.0].</p>
<dl class="docutils">
<dt>Hard priors are specified as:</dt>
<dd><ul class="first last">
<li><p class="first">required_edges: a list of edge-tuples that must be rpesent</p>
</li>
<li><p class="first">prohibited_edges: a list of edge-tuples that must not be present</p>
</li>
<li><dl class="first docutils">
<dt>constraints: a list of functions that take adjacency matrix as input</dt>
<dd><p class="first last">and return true if constraint met and false otherwise.</p>
</dd>
</dl>
</li>
</ul>
</dd>
</dl>
</div></blockquote>
<p>For more information about calculating prior probabilities via energy
matrices, consult:</p>
<blockquote>
<div><ol class="arabic simple">
<li>Imoto, S. and Higuchi, T. and Goto, T. and Tashiro, K. and Kuhara, S.
and Miyano, S. Combining microarrays and biological knowledge for
estimating gene networks via Bayesian networks. Proc IEEE Comput Soc
Bioinform Conf. 2003, p.104-113.</li>
</ol>
</div></blockquote>
<dl class="method">
<dt id="pebl.prior.Prior.loglikelihood">
<tt class="descname">loglikelihood</tt><big>(</big><em>net</em><big>)</big><a class="headerlink" href="#pebl.prior.Prior.loglikelihood" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the log likelihood of the given network.</p>
<p>Similar to the loglikelihood method of a Conditional Probability
Distribution.</p>
</dd></dl>
</dd></dl>
<dl class="class">
<dt id="pebl.prior.UniformPrior">
<em class="property">class </em><tt class="descclassname">pebl.prior.</tt><tt class="descname">UniformPrior</tt><big>(</big><em>num_nodes</em>, <em>weight=1.0</em><big>)</big><a class="headerlink" href="#pebl.prior.UniformPrior" title="Permalink to this definition">¶</a></dt>
<dd><p>A uniform prior – that is, every edge is equally likely.</p>
</dd></dl>
<dl class="class">
<dt id="pebl.prior.NullPrior">
<em class="property">class </em><tt class="descclassname">pebl.prior.</tt><tt class="descname">NullPrior</tt><big>(</big><em>*args</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#pebl.prior.NullPrior" title="Permalink to this definition">¶</a></dt>
<dd><p>A null prior which returns 0.0 for the loglikelihood.</p>
<p>The name for this object is a bit confusing because the UniformPrior is
often considered the null prior in that it doesn’t favor any edge more than
another. It still favors smaller networks and takes time to calculate the
loglikelihood. This class provides an implementation that simply returns
0.0 for the loglikelihood. It’s a null prior in the sense that the
resulting scores are the same as if you hadn’t used a prior at all.</p>
</dd></dl>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar">
<div class="sphinxsidebarwrapper">
<h4>Previous topic</h4>
<p class="topless"><a href="posterior.html"
title="previous chapter"><tt class="docutils literal docutils literal docutils literal"><span class="pre">posterior</span></tt> – Posterior distribution</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="result.html"
title="next chapter"><tt class="docutils literal"><span class="pre">result</span></tt> – Learner results</a></p>
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/prior.txt"
rel="nofollow">Show Source</a></li>
</ul>
<div id="searchbox" style="display: none">
<h3>Quick search</h3>
<form class="search" action="search.html" method="get">
<input type="text" name="q" size="18" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
<p class="searchtip" style="font-size: 90%">
Enter search terms or a module, class or function name.
</p>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
<a href="result.html" title="result – Learner results"
>next</a> |</li>
<li class="right" >
<a href="posterior.html" title="posterior – Posterior distribution"
>previous</a> |</li>
<li><a href="index.html">Pebl v1.0.1 documentation</a> »</li>
<li><a href="apiref.html" >API Reference</a> »</li>
</ul>
</div>
<div class="footer">
© Copyright 2008, Abhik Shah.
Last updated on Apr 29, 2011.
Created using <a href="http://sphinx.pocoo.org/">Sphinx</a> 1.0.7.
</div>
</body>
</html>
|