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<a href="Bio-module.html">Package Bio</a> ::
Module MaxEntropy
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module MaxEntropy</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.MaxEntropy-pysrc.html">source code</a></span></p>
<p>Maximum Entropy code.</p>
<p>Uses Improved Iterative Scaling: XXX ref</p>
<p># XXX need to define terminology</p>
<!-- ==================== CLASSES ==================== -->
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<span class="summary-type"> </span>
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<a href="Bio.MaxEntropy.MaxEntropy-class.html" class="summary-name">MaxEntropy</a><br />
Holds information for a Maximum Entropy classifier.
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<!-- ==================== FUNCTIONS ==================== -->
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<td align="left"><span class="table-header">Functions</span></td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">list of log probs</span>
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<td><span class="summary-sig"><a href="Bio.MaxEntropy-module.html#calculate" class="summary-sig-name">calculate</a>(<span class="summary-sig-arg">me</span>,
<span class="summary-sig-arg">observation</span>)</span><br />
Calculate the log of the probability for each class.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#calculate">source code</a></span>
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<span class="summary-type">class</span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="classify"></a><span class="summary-sig-name">classify</span>(<span class="summary-sig-arg">me</span>,
<span class="summary-sig-arg">observation</span>)</span><br />
Classify an observation into a class.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#classify">source code</a></span>
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<span class="summary-type">dict of values</span>
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<td><span class="summary-sig"><a href="Bio.MaxEntropy-module.html#_eval_feature_fn" class="summary-sig-name" onclick="show_private();">_eval_feature_fn</a>(<span class="summary-sig-arg">fn</span>,
<span class="summary-sig-arg">xs</span>,
<span class="summary-sig-arg">classes</span>)</span><br />
Evaluate a feature function on every instance of the training set and
class.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_eval_feature_fn">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">list of expectations</span>
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<td><span class="summary-sig"><a href="Bio.MaxEntropy-module.html#_calc_empirical_expects" class="summary-sig-name" onclick="show_private();">_calc_empirical_expects</a>(<span class="summary-sig-arg">xs</span>,
<span class="summary-sig-arg">ys</span>,
<span class="summary-sig-arg">classes</span>,
<span class="summary-sig-arg">features</span>)</span><br />
Calculate the expectation of each function from the data.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_calc_empirical_expects">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">list of expectations</span>
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<td><span class="summary-sig"><a href="Bio.MaxEntropy-module.html#_calc_model_expects" class="summary-sig-name" onclick="show_private();">_calc_model_expects</a>(<span class="summary-sig-arg">xs</span>,
<span class="summary-sig-arg">classes</span>,
<span class="summary-sig-arg">features</span>,
<span class="summary-sig-arg">alphas</span>)</span><br />
Calculate the expectation of each feature from the model.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_calc_model_expects">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">matrix</span>
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<td><span class="summary-sig"><a href="Bio.MaxEntropy-module.html#_calc_p_class_given_x" class="summary-sig-name" onclick="show_private();">_calc_p_class_given_x</a>(<span class="summary-sig-arg">xs</span>,
<span class="summary-sig-arg">classes</span>,
<span class="summary-sig-arg">features</span>,
<span class="summary-sig-arg">alphas</span>)</span><br />
Calculate P(y|x), where y is the class and x is an instance from the
training set.</td>
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<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_calc_p_class_given_x">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">matrix of f sharp values.</span>
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<td><span class="summary-sig"><a name="_calc_f_sharp"></a><span class="summary-sig-name">_calc_f_sharp</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">nclasses</span>,
<span class="summary-sig-arg">features</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_calc_f_sharp">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_iis_solve_delta"></a><span class="summary-sig-name">_iis_solve_delta</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">feature</span>,
<span class="summary-sig-arg">f_sharp</span>,
<span class="summary-sig-arg">empirical</span>,
<span class="summary-sig-arg">prob_yx</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_iis_solve_delta">source code</a></span>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_train_iis"></a><span class="summary-sig-name">_train_iis</span>(<span class="summary-sig-arg">xs</span>,
<span class="summary-sig-arg">classes</span>,
<span class="summary-sig-arg">features</span>,
<span class="summary-sig-arg">f_sharp</span>,
<span class="summary-sig-arg">alphas</span>,
<span class="summary-sig-arg">e_empirical</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_train_iis">source code</a></span>
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<span class="summary-type">MaxEntropy object</span>
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<td><span class="summary-sig"><a href="Bio.MaxEntropy-module.html#train" class="summary-sig-name">train</a>(<span class="summary-sig-arg">training_set</span>,
<span class="summary-sig-arg">results</span>,
<span class="summary-sig-arg">feature_fns</span>,
<span class="summary-sig-arg">update_fn</span>=<span class="summary-sig-default">...</span>)</span><br />
Train a maximum entropy classifier on a training set.</td>
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<span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#train">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
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<td align="left"><span class="table-header">Variables</span></td>
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class="privatelink" onclick="toggle_private();"
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<span class="summary-type"> </span>
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<a name="MAX_IIS_ITERATIONS"></a><span class="summary-name">MAX_IIS_ITERATIONS</span> = <code title="10000">10000</code>
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<span class="summary-type"> </span>
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<a name="IIS_CONVERGE"></a><span class="summary-name">IIS_CONVERGE</span> = <code title="1e-05">1e-05</code>
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<span class="summary-type"> </span>
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<a name="MAX_NEWTON_ITERATIONS"></a><span class="summary-name">MAX_NEWTON_ITERATIONS</span> = <code title="100">100</code>
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<span class="summary-type"> </span>
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<a name="NEWTON_CONVERGE"></a><span class="summary-name">NEWTON_CONVERGE</span> = <code title="1e-10">1e-10</code>
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<span class="summary-type"> </span>
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<a name="Complex0"></a><span class="summary-name">Complex0</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="Complex16"></a><span class="summary-name">Complex16</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="Complex32"></a><span class="summary-name">Complex32</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="Complex64"></a><span class="summary-name">Complex64</span> = <code title="'D'"><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code></code>
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<a name="Complex8"></a><span class="summary-name">Complex8</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="Float0"></a><span class="summary-name">Float0</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="Float16"></a><span class="summary-name">Float16</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="Float32"></a><span class="summary-name">Float32</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="Float64"></a><span class="summary-name">Float64</span> = <code title="'d'"><code class="variable-quote">'</code><code class="variable-string">d</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="Float8"></a><span class="summary-name">Float8</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
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<a name="Int0"></a><span class="summary-name">Int0</span> = <code title="'1'"><code class="variable-quote">'</code><code class="variable-string">1</code><code class="variable-quote">'</code></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int16"></a><span class="summary-name">Int16</span> = <code title="'s'"><code class="variable-quote">'</code><code class="variable-string">s</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int32"></a><span class="summary-name">Int32</span> = <code title="'i'"><code class="variable-quote">'</code><code class="variable-string">i</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int64"></a><span class="summary-name">Int64</span> = <code title="'l'"><code class="variable-quote">'</code><code class="variable-string">l</code><code class="variable-quote">'</code></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int8"></a><span class="summary-name">Int8</span> = <code title="'1'"><code class="variable-quote">'</code><code class="variable-string">1</code><code class="variable-quote">'</code></code>
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<a name="absolute"></a><span class="summary-name">absolute</span> = <code title="<ufunc 'absolute'>"><ufunc 'absolute'></code>
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<a name="add"></a><span class="summary-name">add</span> = <code title="<ufunc 'add'>"><ufunc 'add'></code>
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<span class="summary-type"> </span>
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<a name="arccos"></a><span class="summary-name">arccos</span> = <code title="<ufunc 'arccos'>"><ufunc 'arccos'></code>
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<span class="summary-type"> </span>
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<a name="arccosh"></a><span class="summary-name">arccosh</span> = <code title="<ufunc 'arccosh'>"><ufunc 'arccosh'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="arcsin"></a><span class="summary-name">arcsin</span> = <code title="<ufunc 'arcsin'>"><ufunc 'arcsin'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="arcsinh"></a><span class="summary-name">arcsinh</span> = <code title="<ufunc 'arcsinh'>"><ufunc 'arcsinh'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="arctan"></a><span class="summary-name">arctan</span> = <code title="<ufunc 'arctan'>"><ufunc 'arctan'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="arctan2"></a><span class="summary-name">arctan2</span> = <code title="<ufunc 'arctan2'>"><ufunc 'arctan2'></code>
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<span class="summary-type"> </span>
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<a name="arctanh"></a><span class="summary-name">arctanh</span> = <code title="<ufunc 'arctanh'>"><ufunc 'arctanh'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="bitwise_and"></a><span class="summary-name">bitwise_and</span> = <code title="<ufunc 'bitwise_and'>"><ufunc 'bitwise_and'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="bitwise_or"></a><span class="summary-name">bitwise_or</span> = <code title="<ufunc 'bitwise_or'>"><ufunc 'bitwise_or'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="bitwise_xor"></a><span class="summary-name">bitwise_xor</span> = <code title="<ufunc 'bitwise_xor'>"><ufunc 'bitwise_xor'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="ceil"></a><span class="summary-name">ceil</span> = <code title="<ufunc 'ceil'>"><ufunc 'ceil'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="conjugate"></a><span class="summary-name">conjugate</span> = <code title="<ufunc 'conjugate'>"><ufunc 'conjugate'></code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="cos"></a><span class="summary-name">cos</span> = <code title="<ufunc 'cos'>"><ufunc 'cos'></code>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="cosh"></a><span class="summary-name">cosh</span> = <code title="<ufunc 'cosh'>"><ufunc 'cosh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="divide"></a><span class="summary-name">divide</span> = <code title="<ufunc 'divide'>"><ufunc 'divide'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="divide_safe"></a><span class="summary-name">divide_safe</span> = <code title="<ufunc 'divide_safe'>"><ufunc 'divide_safe'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="e"></a><span class="summary-name">e</span> = <code title="2.71828182846">2.71828182846</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="equal"></a><span class="summary-name">equal</span> = <code title="<ufunc 'equal'>"><ufunc 'equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="exp"></a><span class="summary-name">exp</span> = <code title="<ufunc 'exp'>"><ufunc 'exp'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="fabs"></a><span class="summary-name">fabs</span> = <code title="<ufunc 'fabs'>"><ufunc 'fabs'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="floor"></a><span class="summary-name">floor</span> = <code title="<ufunc 'floor'>"><ufunc 'floor'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="floor_divide"></a><span class="summary-name">floor_divide</span> = <code title="<ufunc 'floor_divide'>"><ufunc 'floor_divide'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="fmod"></a><span class="summary-name">fmod</span> = <code title="<ufunc 'fmod'>"><ufunc 'fmod'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="greater"></a><span class="summary-name">greater</span> = <code title="<ufunc 'greater'>"><ufunc 'greater'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="greater_equal"></a><span class="summary-name">greater_equal</span> = <code title="<ufunc 'greater_equal'>"><ufunc 'greater_equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="hypot"></a><span class="summary-name">hypot</span> = <code title="<ufunc 'hypot'>"><ufunc 'hypot'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="invert"></a><span class="summary-name">invert</span> = <code title="<ufunc 'invert'>"><ufunc 'invert'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="left_shift"></a><span class="summary-name">left_shift</span> = <code title="<ufunc 'left_shift'>"><ufunc 'left_shift'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="less"></a><span class="summary-name">less</span> = <code title="<ufunc 'less'>"><ufunc 'less'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="less_equal"></a><span class="summary-name">less_equal</span> = <code title="<ufunc 'less_equal'>"><ufunc 'less_equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="log"></a><span class="summary-name">log</span> = <code title="<ufunc 'log'>"><ufunc 'log'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="log10"></a><span class="summary-name">log10</span> = <code title="<ufunc 'log10'>"><ufunc 'log10'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_and"></a><span class="summary-name">logical_and</span> = <code title="<ufunc 'logical_and'>"><ufunc 'logical_and'></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_not"></a><span class="summary-name">logical_not</span> = <code title="<ufunc 'logical_not'>"><ufunc 'logical_not'></code>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_or"></a><span class="summary-name">logical_or</span> = <code title="<ufunc 'logical_or'>"><ufunc 'logical_or'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_xor"></a><span class="summary-name">logical_xor</span> = <code title="<ufunc 'logical_xor'>"><ufunc 'logical_xor'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="maximum"></a><span class="summary-name">maximum</span> = <code title="<ufunc 'maximum'>"><ufunc 'maximum'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="minimum"></a><span class="summary-name">minimum</span> = <code title="<ufunc 'minimum'>"><ufunc 'minimum'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="multiply"></a><span class="summary-name">multiply</span> = <code title="<ufunc 'multiply'>"><ufunc 'multiply'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="negative"></a><span class="summary-name">negative</span> = <code title="<ufunc 'negative'>"><ufunc 'negative'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="not_equal"></a><span class="summary-name">not_equal</span> = <code title="<ufunc 'not_equal'>"><ufunc 'not_equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="pi"></a><span class="summary-name">pi</span> = <code title="3.14159265359">3.14159265359</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="power"></a><span class="summary-name">power</span> = <code title="<ufunc 'power'>"><ufunc 'power'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="remainder"></a><span class="summary-name">remainder</span> = <code title="<ufunc 'remainder'>"><ufunc 'remainder'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="right_shift"></a><span class="summary-name">right_shift</span> = <code title="<ufunc 'right_shift'>"><ufunc 'right_shift'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sin"></a><span class="summary-name">sin</span> = <code title="<ufunc 'sin'>"><ufunc 'sin'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sinh"></a><span class="summary-name">sinh</span> = <code title="<ufunc 'sinh'>"><ufunc 'sinh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sqrt"></a><span class="summary-name">sqrt</span> = <code title="<ufunc 'sqrt'>"><ufunc 'sqrt'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="subtract"></a><span class="summary-name">subtract</span> = <code title="<ufunc 'subtract'>"><ufunc 'subtract'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="tan"></a><span class="summary-name">tan</span> = <code title="<ufunc 'tan'>"><ufunc 'tan'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="tanh"></a><span class="summary-name">tanh</span> = <code title="<ufunc 'tanh'>"><ufunc 'tanh'></code>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="true_divide"></a><span class="summary-name">true_divide</span> = <code title="<ufunc 'true_divide'>"><ufunc 'true_divide'></code>
</td>
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<!-- ==================== FUNCTION DETAILS ==================== -->
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<a name="calculate"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">calculate</span>(<span class="sig-arg">me</span>,
<span class="sig-arg">observation</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#calculate">source code</a></span>
</td>
</tr></table>
<p>Calculate the log of the probability for each class. me is a
MaxEntropy object that has been trained. observation is a vector
representing the observed data. The return value is a list of
unnormalized log probabilities for each class.</p>
<dl class="fields">
<dt>Returns: list of log probs</dt>
</dl>
</td></tr></table>
</div>
<a name="_eval_feature_fn"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_eval_feature_fn</span>(<span class="sig-arg">fn</span>,
<span class="sig-arg">xs</span>,
<span class="sig-arg">classes</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_eval_feature_fn">source code</a></span>
</td>
</tr></table>
<p>Evaluate a feature function on every instance of the training set and
class. fn is a callback function that takes two parameters: a training
instance and a class. Return a dictionary of (training set index, class
index) -> non-zero value. Values of 0 are not stored in the
dictionary.</p>
<dl class="fields">
<dt>Returns: dict of values</dt>
</dl>
</td></tr></table>
</div>
<a name="_calc_empirical_expects"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_calc_empirical_expects</span>(<span class="sig-arg">xs</span>,
<span class="sig-arg">ys</span>,
<span class="sig-arg">classes</span>,
<span class="sig-arg">features</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_calc_empirical_expects">source code</a></span>
</td>
</tr></table>
<p>Calculate the expectation of each function from the data. This is the
constraint for the maximum entropy distribution. Return a list of
expectations, parallel to the list of features.</p>
<dl class="fields">
<dt>Returns: list of expectations</dt>
</dl>
</td></tr></table>
</div>
<a name="_calc_model_expects"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_calc_model_expects</span>(<span class="sig-arg">xs</span>,
<span class="sig-arg">classes</span>,
<span class="sig-arg">features</span>,
<span class="sig-arg">alphas</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_calc_model_expects">source code</a></span>
</td>
</tr></table>
<p>Calculate the expectation of each feature from the model. This is not
used in maximum entropy training, but provides a good function for
debugging.</p>
<dl class="fields">
<dt>Returns: list of expectations</dt>
</dl>
</td></tr></table>
</div>
<a name="_calc_p_class_given_x"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_calc_p_class_given_x</span>(<span class="sig-arg">xs</span>,
<span class="sig-arg">classes</span>,
<span class="sig-arg">features</span>,
<span class="sig-arg">alphas</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#_calc_p_class_given_x">source code</a></span>
</td>
</tr></table>
<p>Calculate P(y|x), where y is the class and x is an instance from the
training set. Return a XSxCLASSES matrix of probabilities.</p>
<dl class="fields">
<dt>Returns: matrix</dt>
</dl>
</td></tr></table>
</div>
<a name="train"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">train</span>(<span class="sig-arg">training_set</span>,
<span class="sig-arg">results</span>,
<span class="sig-arg">feature_fns</span>,
<span class="sig-arg">update_fn</span>=<span class="sig-default">...</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MaxEntropy-pysrc.html#train">source code</a></span>
</td>
</tr></table>
<p>Train a maximum entropy classifier on a training set. training_set is
a list of observations. results is a list of the class assignments for
each observation. feature_fns is a list of the features. These are
callback functions that take an observation and class and return a 1 or
0. update_fn is a callback function that's called at each training
iteration. It is passed a MaxEntropy object that encapsulates the
current state of the training.</p>
<dl class="fields">
<dt>Returns: MaxEntropy object</dt>
</dl>
</td></tr></table>
</div>
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