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<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../usage.html">Tutorial: Simple DeepProg model</a></li>
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<div class="section" id="simdeep-package">
<h1>simdeep package<a class="headerlink" href="#simdeep-package" title="Permalink to this headline">¶</a></h1>
<div class="section" id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="module-simdeep.config">
<span id="simdeep-config-module"></span><h2>simdeep.config module<a class="headerlink" href="#module-simdeep.config" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="module-simdeep.coxph_from_r">
<span id="simdeep-coxph-from-r-module"></span><h2>simdeep.coxph_from_r module<a class="headerlink" href="#module-simdeep.coxph_from_r" title="Permalink to this headline">¶</a></h2>
<dl class="py function">
<dt id="simdeep.coxph_from_r.c_index">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">c_index</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">values</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">values_test</span></em>, <em class="sig-param"><span class="n">isdead_test</span></em>, <em class="sig-param"><span class="n">nbdays_test</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">use_r_packages</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">seed</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#c_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.c_index" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.c_index_from_python">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">c_index_from_python</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">values</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">values_test</span></em>, <em class="sig-param"><span class="n">isdead_test</span></em>, <em class="sig-param"><span class="n">nbdays_test</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#c_index_from_python"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.c_index_from_python" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.c_index_from_r">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">c_index_from_r</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">values</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">values_test</span></em>, <em class="sig-param"><span class="n">isdead_test</span></em>, <em class="sig-param"><span class="n">nbdays_test</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#c_index_from_r"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.c_index_from_r" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.c_index_multiple">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">c_index_multiple</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">values</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">values_test</span></em>, <em class="sig-param"><span class="n">isdead_test</span></em>, <em class="sig-param"><span class="n">nbdays_test</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">use_r_packages</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">seed</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#c_index_multiple"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.c_index_multiple" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.c_index_multiple_from_python">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">c_index_multiple_from_python</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">matrix</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">matrix_test</span></em>, <em class="sig-param"><span class="n">isdead_test</span></em>, <em class="sig-param"><span class="n">nbdays_test</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#c_index_multiple_from_python"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.c_index_multiple_from_python" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.c_index_multiple_from_r">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">c_index_multiple_from_r</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">matrix</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">matrix_test</span></em>, <em class="sig-param"><span class="n">isdead_test</span></em>, <em class="sig-param"><span class="n">nbdays_test</span></em>, <em class="sig-param"><span class="n">lambda_val</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#c_index_multiple_from_r"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.c_index_multiple_from_r" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.convert_to_rmatrix">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">convert_to_rmatrix</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">data</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#convert_to_rmatrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.convert_to_rmatrix" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.coxph">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">coxph</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">values</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">do_KM_plot</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">metadata_mat</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">png_path</span><span class="o">=</span><span class="default_value">'./'</span></em>, <em class="sig-param"><span class="n">dichotomize_afterward</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">fig_name</span><span class="o">=</span><span class="default_value">'KM_plot.png'</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">use_r_packages</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">seed</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#coxph"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.coxph" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.coxph_from_python">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">coxph_from_python</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">values</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">do_KM_plot</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">png_path</span><span class="o">=</span><span class="default_value">'./'</span></em>, <em class="sig-param"><span class="n">metadata_mat</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">dichotomize_afterward</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">fig_name</span><span class="o">=</span><span class="default_value">'KM_plot.pdf'</span></em>, <em class="sig-param"><span class="n">penalizer</span><span class="o">=</span><span class="default_value">0.01</span></em>, <em class="sig-param"><span class="n">l1_ratio</span><span class="o">=</span><span class="default_value">0.0</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#coxph_from_python"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.coxph_from_python" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.coxph_from_r">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">coxph_from_r</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">values</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">do_KM_plot</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">metadata_mat</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">png_path</span><span class="o">=</span><span class="default_value">'./'</span></em>, <em class="sig-param"><span class="n">dichotomize_afterward</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">fig_name</span><span class="o">=</span><span class="default_value">'KM_plot.png'</span></em>, <em class="sig-param"><span class="n">isfactor</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#coxph_from_r"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.coxph_from_r" title="Permalink to this definition">¶</a></dt>
<dd><dl class="simple">
<dt>input:</dt><dd><dl class="field-list simple">
<dt class="field-odd">values</dt>
<dd class="field-odd"><p>array values of activities</p>
</dd>
<dt class="field-even">isdead</dt>
<dd class="field-even"><p>array <binary> Event occured int boolean: 0/1</p>
</dd>
<dt class="field-odd">nbdays</dt>
<dd class="field-odd"><p>array <int></p>
</dd>
</dl>
</dd>
<dt>return:</dt><dd><p>pvalues from wald test</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.main">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.main" title="Permalink to this definition">¶</a></dt>
<dd><p>DEBUG</p>
</dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.predict_with_coxph_glmnet">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">predict_with_coxph_glmnet</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">matrix</span></em>, <em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">matrix_test</span></em>, <em class="sig-param"><span class="n">alpha</span><span class="o">=</span><span class="default_value">0.5</span></em>, <em class="sig-param"><span class="n">lambda_val</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#predict_with_coxph_glmnet"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.predict_with_coxph_glmnet" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.surv_mean">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">surv_mean</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">use_r_packages</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#surv_mean"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.surv_mean" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.surv_mean_from_python">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">surv_mean_from_python</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#surv_mean_from_python"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.surv_mean_from_python" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.surv_mean_from_r">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">surv_mean_from_r</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#surv_mean_from_r"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.surv_mean_from_r" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.surv_median">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">surv_median</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em>, <em class="sig-param"><span class="n">use_r_packages</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#surv_median"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.surv_median" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.surv_median_from_python">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">surv_median_from_python</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#surv_median_from_python"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.surv_median_from_python" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.coxph_from_r.surv_median_from_r">
<code class="sig-prename descclassname">simdeep.coxph_from_r.</code><code class="sig-name descname">surv_median_from_r</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">isdead</span></em>, <em class="sig-param"><span class="n">nbdays</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/coxph_from_r.html#surv_median_from_r"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.coxph_from_r.surv_median_from_r" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</div>
<div class="section" id="module-simdeep.deepmodel_base">
<span id="simdeep-deepmodel-base-module"></span><h2>simdeep.deepmodel_base module<a class="headerlink" href="#module-simdeep.deepmodel_base" title="Permalink to this headline">¶</a></h2>
<dl class="py class">
<dt id="simdeep.deepmodel_base.DeepBase">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.deepmodel_base.</code><code class="sig-name descname">DeepBase</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">epochs</span><span class="o">=</span><span class="default_value">10</span></em>, <em class="sig-param"><span class="n">level_dims_in</span><span class="o">=</span><span class="default_value">()</span></em>, <em class="sig-param"><span class="n">level_dims_out</span><span class="o">=</span><span class="default_value">()</span></em>, <em class="sig-param"><span class="n">new_dim</span><span class="o">=</span><span class="default_value">100</span></em>, <em class="sig-param"><span class="n">loss</span><span class="o">=</span><span class="default_value">'binary_crossentropy'</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="o">=</span><span class="default_value">'adam'</span></em>, <em class="sig-param"><span class="n">act_reg</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">w_reg</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">dropout</span><span class="o">=</span><span class="default_value">0.5</span></em>, <em class="sig-param"><span class="n">data_split</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">activation</span><span class="o">=</span><span class="default_value">'tanh'</span></em>, <em class="sig-param"><span class="n">seed</span><span class="o">=</span><span class="default_value">2020</span></em>, <em class="sig-param"><span class="n">alternative_embedding</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">kwargs_alternative_embedding</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="n">path_to_save_model</span><span class="o">=</span><span class="default_value">'./'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.compile_models">
<code class="sig-name descname">compile_models</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.compile_models"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.compile_models" title="Permalink to this definition">¶</a></dt>
<dd><p>define the optimizer and the loss function
compile the model and ready to fit the data!</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.construct_autoencoders">
<code class="sig-name descname">construct_autoencoders</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.construct_autoencoders"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.construct_autoencoders" title="Permalink to this definition">¶</a></dt>
<dd><p>main class to create the autoencoder</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.construct_supervized_network">
<code class="sig-name descname">construct_supervized_network</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">objective</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.construct_supervized_network"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.construct_supervized_network" title="Permalink to this definition">¶</a></dt>
<dd><p>main class to create the autoencoder</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.create_autoencoders">
<code class="sig-name descname">create_autoencoders</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">matrix_out</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.create_autoencoders"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.create_autoencoders" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.embedding_predict">
<code class="sig-name descname">embedding_predict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">key</span></em>, <em class="sig-param"><span class="n">matrix</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.embedding_predict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.embedding_predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Predict the output value using the matrix as input and
the fitted embedding model from self.alternative_embedding_array</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.encoder_input_shape">
<code class="sig-name descname">encoder_input_shape</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">key</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.encoder_input_shape"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.encoder_input_shape" title="Permalink to this definition">¶</a></dt>
<dd><p>Predict the output value using the matrix as input for the encoder from key</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.encoder_predict">
<code class="sig-name descname">encoder_predict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">key</span></em>, <em class="sig-param"><span class="n">matrix</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.encoder_predict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.encoder_predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Predict the output value using the matrix as input for the encoder from key</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.fit_alternative_embedding">
<code class="sig-name descname">fit_alternative_embedding</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.fit_alternative_embedding"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.fit_alternative_embedding" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.fit_autoencoders">
<code class="sig-name descname">fit_autoencoders</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">objective</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.fit_autoencoders"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.fit_autoencoders" title="Permalink to this definition">¶</a></dt>
<dd><p>fit the autoencoder using the training matrix</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.load_encoders">
<code class="sig-name descname">load_encoders</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">fname</span><span class="o">=</span><span class="default_value">'encoder.h5'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.load_encoders"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.load_encoders" title="Permalink to this definition">¶</a></dt>
<dd><p>Load a keras model from the self.path_to_save_model directory
:fname: str the name of the file to load</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.load_test_dataset">
<code class="sig-name descname">load_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.load_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.load_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>load test dataset and test surival</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.load_training_dataset">
<code class="sig-name descname">load_training_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.load_training_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.load_training_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>load training dataset and surival</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.deepmodel_base.DeepBase.save_encoders">
<code class="sig-name descname">save_encoders</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">fname</span><span class="o">=</span><span class="default_value">'encoder.h5'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#DeepBase.save_encoders"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.DeepBase.save_encoders" title="Permalink to this definition">¶</a></dt>
<dd><p>Save a keras model in the self.path_to_save_model directory
:fname: str the name of the file to save the model</p>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt id="simdeep.deepmodel_base.main">
<code class="sig-prename descclassname">simdeep.deepmodel_base.</code><code class="sig-name descname">main</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/deepmodel_base.html#main"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.deepmodel_base.main" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</div>
<div class="section" id="module-simdeep.extract_data">
<span id="simdeep-extract-data-module"></span><h2>simdeep.extract_data module<a class="headerlink" href="#module-simdeep.extract_data" title="Permalink to this headline">¶</a></h2>
<dl class="py class">
<dt id="simdeep.extract_data.LoadData">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.extract_data.</code><code class="sig-name descname">LoadData</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_data</span><span class="o">=</span><span class="default_value">'/home/oliver/code/SimDeep/simdeep/../examples/data/'</span></em>, <em class="sig-param"><span class="n">training_tsv</span><span class="o">=</span><span class="default_value">{'GE': 'rna_dummy.tsv', 'METH': 'meth_dummy.tsv', 'MIR': 'mir_dummy.tsv'}</span></em>, <em class="sig-param"><span class="n">survival_tsv</span><span class="o">=</span><span class="default_value">'survival_dummy.tsv'</span></em>, <em class="sig-param"><span class="n">metadata_tsv</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">metadata_test_tsv</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">test_tsv</span><span class="o">=</span><span class="default_value">{'MIR': 'mir_test_dummy.tsv'}</span></em>, <em class="sig-param"><span class="n">survival_tsv_test</span><span class="o">=</span><span class="default_value">'survival_test_dummy.tsv'</span></em>, <em class="sig-param"><span class="n">cross_validation_instance</span><span class="o">=</span><span class="default_value">KFold(n_splits=5, random_state=1, shuffle=True)</span></em>, <em class="sig-param"><span class="n">test_fold</span><span class="o">=</span><span class="default_value">0</span></em>, <em class="sig-param"><span class="n">stack_multi_omic</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">fill_unkown_feature_with_0</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">normalization</span><span class="o">=</span><span class="default_value">{'NB_FEATURES_TO_KEEP': 100, 'TRAIN_CORR_RANK_NORM': True, 'TRAIN_CORR_REDUCTION': True, 'TRAIN_MAD_SCALE': False, 'TRAIN_MIN_MAX': False, 'TRAIN_NORM_SCALE': False, 'TRAIN_QUANTILE_TRANSFORM': False, 'TRAIN_RANK_NORM': True, 'TRAIN_ROBUST_SCALE': False, 'TRAIN_ROBUST_SCALE_TWO_WAY': False}</span></em>, <em class="sig-param"><span class="n">survival_flag</span><span class="o">=</span><span class="default_value">{'event': 'recurrence', 'patient_id': 'barcode', 'survival': 'days'}</span></em>, <em class="sig-param"><span class="n">subset_training_with_meta</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="n">_autoencoder_parameters</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.create_a_cv_split">
<code class="sig-name descname">create_a_cv_split</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.create_a_cv_split"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.create_a_cv_split" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_array">
<code class="sig-name descname">load_array</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_array" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_matrix_full">
<code class="sig-name descname">load_matrix_full</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_matrix_full"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_matrix_full" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_matrix_test">
<code class="sig-name descname">load_matrix_test</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">normalization</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_matrix_test"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_matrix_test" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_matrix_test_fold">
<code class="sig-name descname">load_matrix_test_fold</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_matrix_test_fold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_matrix_test_fold" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_meta_data">
<code class="sig-name descname">load_meta_data</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">sep</span><span class="o">=</span><span class="default_value">'\t'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_meta_data"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_meta_data" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_meta_data_test">
<code class="sig-name descname">load_meta_data_test</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">metadata_file</span><span class="o">=</span><span class="default_value">''</span></em>, <em class="sig-param"><span class="n">sep</span><span class="o">=</span><span class="default_value">'\t'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_meta_data_test"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_meta_data_test" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_new_test_dataset">
<code class="sig-name descname">load_new_test_dataset</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">tsv_dict</span></em>, <em class="sig-param"><span class="n">path_survival_file</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">survival_flag</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">normalization</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">metadata_file</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_new_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_new_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_survival">
<code class="sig-name descname">load_survival</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_survival"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_survival" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.load_survival_test">
<code class="sig-name descname">load_survival_test</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">survival_flag</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.load_survival_test"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.load_survival_test" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.normalize_training_array">
<code class="sig-name descname">normalize_training_array</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.normalize_training_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.normalize_training_array" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.reorder_matrix_array">
<code class="sig-name descname">reorder_matrix_array</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">new_sample_ids</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.reorder_matrix_array"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.reorder_matrix_array" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.save_ref_matrix">
<code class="sig-name descname">save_ref_matrix</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_folder</span></em>, <em class="sig-param"><span class="n">project_name</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.save_ref_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.save_ref_matrix" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.subset_training_sets">
<code class="sig-name descname">subset_training_sets</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">change_cv</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.subset_training_sets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.subset_training_sets" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.extract_data.LoadData.transform_matrices">
<code class="sig-name descname">transform_matrices</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">matrix_ref</span></em>, <em class="sig-param"><span class="n">matrix</span></em>, <em class="sig-param"><span class="n">key</span></em>, <em class="sig-param"><span class="n">normalization</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/extract_data.html#LoadData.transform_matrices"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.extract_data.LoadData.transform_matrices" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
</div>
<div class="section" id="module-simdeep.plot_utils">
<span id="simdeep-plot-utils-module"></span><h2>simdeep.plot_utils module<a class="headerlink" href="#module-simdeep.plot_utils" title="Permalink to this headline">¶</a></h2>
<dl class="py class">
<dt id="simdeep.plot_utils.SampleHTML">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.plot_utils.</code><code class="sig-name descname">SampleHTML</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">name</span></em>, <em class="sig-param"><span class="n">label</span></em>, <em class="sig-param"><span class="n">proba</span></em>, <em class="sig-param"><span class="n">survival</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/plot_utils.html#SampleHTML"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.plot_utils.SampleHTML" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
</dd></dl>
<dl class="py function">
<dt id="simdeep.plot_utils.make_color_dict">
<code class="sig-prename descclassname">simdeep.plot_utils.</code><code class="sig-name descname">make_color_dict</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">id_list</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/plot_utils.html#make_color_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.plot_utils.make_color_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>According to an id_list define a color gradient
return {id:color}</p>
</dd></dl>
<dl class="py function">
<dt id="simdeep.plot_utils.make_color_dict_from_r">
<code class="sig-prename descclassname">simdeep.plot_utils.</code><code class="sig-name descname">make_color_dict_from_r</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">labels</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/plot_utils.html#make_color_dict_from_r"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.plot_utils.make_color_dict_from_r" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.plot_utils.make_color_list">
<code class="sig-prename descclassname">simdeep.plot_utils.</code><code class="sig-name descname">make_color_list</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">id_list</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/plot_utils.html#make_color_list"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.plot_utils.make_color_list" title="Permalink to this definition">¶</a></dt>
<dd><p>According to an id_list define a color gradient
return {id:color}</p>
</dd></dl>
<dl class="py function">
<dt id="simdeep.plot_utils.plot_kernel_plots">
<code class="sig-prename descclassname">simdeep.plot_utils.</code><code class="sig-name descname">plot_kernel_plots</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">test_labels</span></em>, <em class="sig-param"><span class="n">test_labels_proba</span></em>, <em class="sig-param"><span class="n">labels</span></em>, <em class="sig-param"><span class="n">activities</span></em>, <em class="sig-param"><span class="n">activities_test</span></em>, <em class="sig-param"><span class="n">dataset</span></em>, <em class="sig-param"><span class="n">path_html</span></em>, <em class="sig-param"><span class="n">metadata_frame</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/plot_utils.html#plot_kernel_plots"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.plot_utils.plot_kernel_plots" title="Permalink to this definition">¶</a></dt>
<dd><p>perform a html kernel plot</p>
</dd></dl>
</div>
<div class="section" id="module-simdeep.simdeep_analysis">
<span id="simdeep-simdeep-analysis-module"></span><h2>simdeep.simdeep_analysis module<a class="headerlink" href="#module-simdeep.simdeep_analysis" title="Permalink to this headline">¶</a></h2>
<p>DeepProg class for one instance model</p>
<dl class="py class">
<dt id="simdeep.simdeep_analysis.SimDeep">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.simdeep_analysis.</code><code class="sig-name descname">SimDeep</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">nb_clusters</span><span class="o">=</span><span class="default_value">2</span></em>, <em class="sig-param"><span class="n">pvalue_thres</span><span class="o">=</span><span class="default_value">0.01</span></em>, <em class="sig-param"><span class="n">cindex_thres</span><span class="o">=</span><span class="default_value">0.65</span></em>, <em class="sig-param"><span class="n">use_autoencoders</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">feature_surv_analysis</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">cluster_method</span><span class="o">=</span><span class="default_value">'mixture'</span></em>, <em class="sig-param"><span class="n">cluster_eval_method</span><span class="o">=</span><span class="default_value">'silhouette'</span></em>, <em class="sig-param"><span class="n">classifier_type</span><span class="o">=</span><span class="default_value">'svm'</span></em>, <em class="sig-param"><span class="n">project_name</span><span class="o">=</span><span class="default_value">'test_dummy_dataset'</span></em>, <em class="sig-param"><span class="n">path_results</span><span class="o">=</span><span class="default_value">'./'</span></em>, <em class="sig-param"><span class="n">cluster_array</span><span class="o">=</span><span class="default_value">[]</span></em>, <em class="sig-param"><span class="n">nb_selected_features</span><span class="o">=</span><span class="default_value">50</span></em>, <em class="sig-param"><span class="n">mixture_params</span><span class="o">=</span><span class="default_value">{'covariance_type': 'diag', 'max_iter': 1000, 'n_init': 100}</span></em>, <em class="sig-param"><span class="n">node_selection</span><span class="o">=</span><span class="default_value">'Cox-PH'</span></em>, <em class="sig-param"><span class="n">nb_threads_coxph</span><span class="o">=</span><span class="default_value">10</span></em>, <em class="sig-param"><span class="n">classification_method</span><span class="o">=</span><span class="default_value">'ALL_FEATURES'</span></em>, <em class="sig-param"><span class="n">load_existing_models</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">path_to_save_model</span><span class="o">=</span><span class="default_value">'./'</span></em>, <em class="sig-param"><span class="n">clustering_omics</span><span class="o">=</span><span class="default_value">[]</span></em>, <em class="sig-param"><span class="n">metadata_usage</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">feature_selection_usage</span><span class="o">=</span><span class="default_value">'individual'</span></em>, <em class="sig-param"><span class="n">seed</span><span class="o">=</span><span class="default_value">2020</span></em>, <em class="sig-param"><span class="n">alternative_embedding</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">do_KM_plot</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">_isboosting</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">dataset</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">kwargs_alternative_embedding</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="n">deep_model_additional_args</span><span class="o">=</span><span class="default_value">{}</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#simdeep.deepmodel_base.DeepBase" title="simdeep.deepmodel_base.DeepBase"><code class="xref py py-class docutils literal notranslate"><span class="pre">simdeep.deepmodel_base.DeepBase</span></code></a></p>
<p>Instanciate a new DeepProg instance.
The default parameters are defined in the config.py file</p>
<dl class="simple">
<dt>Parameters:</dt><dd><dl class="field-list simple">
<dt class="field-odd">dataset</dt>
<dd class="field-odd"><p>ExtractData instance. Default None (create a new dataset using the config variable)</p>
</dd>
<dt class="field-even">nb_clusters</dt>
<dd class="field-even"><p>Number of clusters to search (default NB_CLUSTERS)</p>
</dd>
<dt class="field-odd">pvalue_thres</dt>
<dd class="field-odd"><p>Pvalue threshold to include a feature (default PVALUE_THRESHOLD)</p>
</dd>
<dt class="field-even">clustering_omics</dt>
<dd class="field-even"><p>Which omics to use for clustering. If empty, then all the available omics will be used</p>
</dd>
<dt class="field-odd">cindex_thres</dt>
<dd class="field-odd"><p>C-index threshold to include a feature. This parameter is used only if <cite>node_selection</cite> is set to “C-index” (default CINDEX_THRESHOLD)</p>
</dd>
<dt class="field-even">cluster_method</dt>
<dd class="field-even"><p>Cluster method to use. possible choice [‘mixture’, ‘kmeans’]. (default CLUSTER_METHOD)</p>
</dd>
<dt class="field-odd">cluster_eval_method</dt>
<dd class="field-odd"><p>Cluster evaluation method to use in case the <cite>cluster_array</cite> parameter is a list of possible K. Possible choice [‘bic’, ‘silhouette’, ‘calinski’] (default CLUSTER_EVAL_METHOD)</p>
</dd>
<dt class="field-even">classifier_type</dt>
<dd class="field-even"><p>Type of classifier to use. Possible choice [‘svm’, ‘clustering’]. If ‘clustering’ is selected, The predict method of the clustering algoritm is used (default CLASSIFIER_TYPE)</p>
</dd>
<dt class="field-odd">project_name</dt>
<dd class="field-odd"><p>Name of the project. This name will be used to save the output files and create the output folder (default PROJECT_NAME)</p>
</dd>
<dt class="field-even">path_results</dt>
<dd class="field-even"><p>Result folder path used to save the output files (default PATH_RESULTS)</p>
</dd>
<dt class="field-odd">cluster_array</dt>
<dd class="field-odd"><p>Array of possible number of clusters to try. If set, <cite>nb_clusters</cite> is ignored (default CLUSTER_ARRAY)</p>
</dd>
<dt class="field-even">nb_selected_features</dt>
<dd class="field-even"><p>Number of selected features to construct classifiers (default NB_SELECTED_FEATURES)</p>
</dd>
<dt class="field-odd">mixture_params</dt>
<dd class="field-odd"><p>Dictionary of parameters used to instanciate the Gaussian mixture algorithm (default MIXTURE_PARAMS)</p>
</dd>
<dt class="field-even">node_selection</dt>
<dd class="field-even"><p>Mehtod to select new features. possible choice [‘Cox-PH’, ‘C-index’]. (default NODES_SELECTION)</p>
</dd>
<dt class="field-odd">nb_threads_coxph</dt>
<dd class="field-odd"><p>Number of python processes to use to compute individual survival models in parallel (default NB_THREADS_COXPH)</p>
</dd>
<dt class="field-even">classification_method</dt>
<dd class="field-even"><p>Possible choice [‘ALL_FEATURES’, ‘SURVIVAL_FEATURES’]. If ‘SURVIVAL_FEATURES’ is selected, the classifiers are built using survival features (default CLASSIFICATION_METHOD)</p>
</dd>
<dt class="field-odd">load_existing_models</dt>
<dd class="field-odd"><p>(default LOAD_EXISTING_MODELS)</p>
</dd>
<dt class="field-even">path_to_save_model</dt>
<dd class="field-even"><p>(default PATH_TO_SAVE_MODEL)</p>
</dd>
<dt class="field-odd">metadata_usage</dt>
<dd class="field-odd"><p>Meta data usage with survival models (if metadata_tsv provided as argument to the dataset). Possible choice are [None, False, ‘labels’, ‘new-features’, ‘all’, True] (True is the same as all)</p>
</dd>
<dt class="field-even">feature_selection_usage</dt>
<dd class="field-even"><p>selection method for survival features (‘individual’ or ‘lasso’)</p>
</dd>
<dt class="field-odd">alternative_embedding</dt>
<dd class="field-odd"><p>alternative external embedding to use instead of builfing autoencoders (default None)</p>
</dd>
<dt class="field-even">kwargs_alternative_embedding</dt>
<dd class="field-even"><p>parameters for external embedding fitting</p>
</dd>
</dl>
</dd>
</dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_full_dataset">
<code class="sig-name descname">compute_c_indexes_for_full_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_c_indexes_for_full_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_full_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_test_dataset">
<code class="sig-name descname">compute_c_indexes_for_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_c_indexes_for_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_test_fold_dataset">
<code class="sig-name descname">compute_c_indexes_for_test_fold_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_c_indexes_for_test_fold_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_test_fold_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_training_dataset">
<code class="sig-name descname">compute_c_indexes_for_training_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_c_indexes_for_training_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_for_training_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_c_indexes_multiple_for_test_dataset">
<code class="sig-name descname">compute_c_indexes_multiple_for_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_c_indexes_multiple_for_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_multiple_for_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_c_indexes_multiple_for_test_fold_dataset">
<code class="sig-name descname">compute_c_indexes_multiple_for_test_fold_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_c_indexes_multiple_for_test_fold_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_c_indexes_multiple_for_test_fold_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using test-fold labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_feature_scores">
<code class="sig-name descname">compute_feature_scores</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">use_ref</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_feature_scores"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_feature_scores" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.compute_feature_scores_per_cluster">
<code class="sig-name descname">compute_feature_scores_per_cluster</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">use_ref</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">pval_thres</span><span class="o">=</span><span class="default_value">0.01</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.compute_feature_scores_per_cluster"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.compute_feature_scores_per_cluster" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.evalutate_cluster_performance">
<code class="sig-name descname">evalutate_cluster_performance</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.evalutate_cluster_performance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.evalutate_cluster_performance" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.fit">
<code class="sig-name descname">fit</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.fit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.fit" title="Permalink to this definition">¶</a></dt>
<dd><p>main function
I) construct an autoencoder or fit alternative embedding
II) predict nodes linked with survival (if active)
and III) do clustering</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.fit_classification_model">
<code class="sig-name descname">fit_classification_model</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.fit_classification_model"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.fit_classification_model" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.fit_classification_test_model">
<code class="sig-name descname">fit_classification_test_model</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.fit_classification_test_model"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.fit_classification_test_model" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.fit_on_pretrained_label_file">
<code class="sig-name descname">fit_on_pretrained_label_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">label_file</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.fit_on_pretrained_label_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.fit_on_pretrained_label_file" title="Permalink to this definition">¶</a></dt>
<dd><p>fit a deepprog simdeep model without training autoencoder but just using a ID->labels file to train a classifier</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.load_new_test_dataset">
<code class="sig-name descname">load_new_test_dataset</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">tsv_dict</span></em>, <em class="sig-param"><span class="n">fname_key</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">path_survival_file</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">normalization</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">survival_flag</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">metadata_file</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.load_new_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.load_new_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.look_for_prediction_nodes">
<code class="sig-name descname">look_for_prediction_nodes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">keys</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.look_for_prediction_nodes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.look_for_prediction_nodes" title="Permalink to this definition">¶</a></dt>
<dd><p>detect nodes from the autoencoder that predict a
high c-index scores using label from the retained test fold</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.look_for_survival_nodes">
<code class="sig-name descname">look_for_survival_nodes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">keys</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.look_for_survival_nodes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.look_for_survival_nodes" title="Permalink to this definition">¶</a></dt>
<dd><p>detect nodes from the autoencoder significantly
linked with survival through coxph regression</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.plot_kernel_for_test_sets">
<code class="sig-name descname">plot_kernel_for_test_sets</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">labels</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">labels_proba</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">test_labels</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">test_labels_proba</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">define_as_main_kernel</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">use_main_kernel</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">activities</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">activities_test</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">key</span><span class="o">=</span><span class="default_value">''</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.plot_kernel_for_test_sets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.plot_kernel_for_test_sets" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.plot_supervised_kernel_for_test_sets">
<code class="sig-name descname">plot_supervised_kernel_for_test_sets</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">labels</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">labels_proba</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">dataset</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">key</span><span class="o">=</span><span class="default_value">''</span></em>, <em class="sig-param"><span class="n">use_main_kernel</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">test_labels</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">test_labels_proba</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">define_as_main_kernel</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.plot_supervised_kernel_for_test_sets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.plot_supervised_kernel_for_test_sets" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.predict_labels">
<code class="sig-name descname">predict_labels</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.predict_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.predict_labels" title="Permalink to this definition">¶</a></dt>
<dd><p>predict labels from training set
using K-Means algorithm on the node activities,
using only nodes linked to survival</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.predict_labels_on_full_dataset">
<code class="sig-name descname">predict_labels_on_full_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.predict_labels_on_full_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.predict_labels_on_full_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.predict_labels_on_test_dataset">
<code class="sig-name descname">predict_labels_on_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.predict_labels_on_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.predict_labels_on_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.predict_labels_on_test_fold">
<code class="sig-name descname">predict_labels_on_test_fold</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.predict_labels_on_test_fold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.predict_labels_on_test_fold" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.predict_labels_using_external_labels">
<code class="sig-name descname">predict_labels_using_external_labels</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">labels</span></em>, <em class="sig-param"><span class="n">labels_proba</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.predict_labels_using_external_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.predict_labels_using_external_labels" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.predict_nodes_activities">
<code class="sig-name descname">predict_nodes_activities</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">matrix_array</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.predict_nodes_activities"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.predict_nodes_activities" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.write_feature_score_per_cluster">
<code class="sig-name descname">write_feature_score_per_cluster</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.write_feature_score_per_cluster"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.write_feature_score_per_cluster" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_analysis.SimDeep.write_feature_scores">
<code class="sig-name descname">write_feature_scores</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_analysis.html#SimDeep.write_feature_scores"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_analysis.SimDeep.write_feature_scores" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
</div>
<div class="section" id="module-simdeep.simdeep_boosting">
<span id="simdeep-simdeep-boosting-module"></span><h2>simdeep.simdeep_boosting module<a class="headerlink" href="#module-simdeep.simdeep_boosting" title="Permalink to this headline">¶</a></h2>
<dl class="py class">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.simdeep_boosting.</code><code class="sig-name descname">SimDeepBoosting</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">nb_it</span><span class="o">=</span><span class="default_value">5</span></em>, <em class="sig-param"><span class="n">do_KM_plot</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">distribute</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">nb_threads</span><span class="o">=</span><span class="default_value">5</span></em>, <em class="sig-param"><span class="n">class_selection</span><span class="o">=</span><span class="default_value">'mean'</span></em>, <em class="sig-param"><span class="n">model_thres</span><span class="o">=</span><span class="default_value">0.05</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">seed</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">project_name</span><span class="o">=</span><span class="default_value">'test_dummy_dataset_boosting'</span></em>, <em class="sig-param"><span class="n">use_autoencoders</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">feature_surv_analysis</span><span class="o">=</span><span class="default_value">True</span></em>, <em class="sig-param"><span class="n">split_n_fold</span><span class="o">=</span><span class="default_value">5</span></em>, <em class="sig-param"><span class="n">path_results</span><span class="o">=</span><span class="default_value">'./'</span></em>, <em class="sig-param"><span class="n">nb_clusters</span><span class="o">=</span><span class="default_value">2</span></em>, <em class="sig-param"><span class="n">epochs</span><span class="o">=</span><span class="default_value">10</span></em>, <em class="sig-param"><span class="n">normalization</span><span class="o">=</span><span class="default_value">{'NB_FEATURES_TO_KEEP': 100, 'TRAIN_CORR_RANK_NORM': True, 'TRAIN_CORR_REDUCTION': True, 'TRAIN_MAD_SCALE': False, 'TRAIN_MIN_MAX': False, 'TRAIN_NORM_SCALE': False, 'TRAIN_QUANTILE_TRANSFORM': False, 'TRAIN_RANK_NORM': True, 'TRAIN_ROBUST_SCALE': False, 'TRAIN_ROBUST_SCALE_TWO_WAY': False}</span></em>, <em class="sig-param"><span class="n">nb_selected_features</span><span class="o">=</span><span class="default_value">50</span></em>, <em class="sig-param"><span class="n">cluster_method</span><span class="o">=</span><span class="default_value">'mixture'</span></em>, <em class="sig-param"><span class="n">pvalue_thres</span><span class="o">=</span><span class="default_value">0.01</span></em>, <em class="sig-param"><span class="n">classification_method</span><span class="o">=</span><span class="default_value">'ALL_FEATURES'</span></em>, <em class="sig-param"><span class="n">new_dim</span><span class="o">=</span><span class="default_value">100</span></em>, <em class="sig-param"><span class="n">training_tsv</span><span class="o">=</span><span class="default_value">{'GE': 'rna_dummy.tsv', 'METH': 'meth_dummy.tsv', 'MIR': 'mir_dummy.tsv'}</span></em>, <em class="sig-param"><span class="n">metadata_usage</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">survival_tsv</span><span class="o">=</span><span class="default_value">'survival_dummy.tsv'</span></em>, <em class="sig-param"><span class="n">metadata_tsv</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">subset_training_with_meta</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="n">survival_flag</span><span class="o">=</span><span class="default_value">{'event': 'recurrence', 'patient_id': 'barcode', 'survival': 'days'}</span></em>, <em class="sig-param"><span class="n">path_data</span><span class="o">=</span><span class="default_value">'/home/oliver/code/SimDeep/simdeep/../examples/data/'</span></em>, <em class="sig-param"><span class="n">level_dims_in</span><span class="o">=</span><span class="default_value">()</span></em>, <em class="sig-param"><span class="n">level_dims_out</span><span class="o">=</span><span class="default_value">()</span></em>, <em class="sig-param"><span class="n">loss</span><span class="o">=</span><span class="default_value">'binary_crossentropy'</span></em>, <em class="sig-param"><span class="n">optimizer</span><span class="o">=</span><span class="default_value">'adam'</span></em>, <em class="sig-param"><span class="n">act_reg</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">w_reg</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">dropout</span><span class="o">=</span><span class="default_value">0.5</span></em>, <em class="sig-param"><span class="n">data_split</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">node_selection</span><span class="o">=</span><span class="default_value">'Cox-PH'</span></em>, <em class="sig-param"><span class="n">cindex_thres</span><span class="o">=</span><span class="default_value">0.65</span></em>, <em class="sig-param"><span class="n">activation</span><span class="o">=</span><span class="default_value">'tanh'</span></em>, <em class="sig-param"><span class="n">clustering_omics</span><span class="o">=</span><span class="default_value">[]</span></em>, <em class="sig-param"><span class="n">path_to_save_model</span><span class="o">=</span><span class="default_value">'./'</span></em>, <em class="sig-param"><span class="n">feature_selection_usage</span><span class="o">=</span><span class="default_value">'individual'</span></em>, <em class="sig-param"><span class="n">alternative_embedding</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">kwargs_alternative_embedding</span><span class="o">=</span><span class="default_value">{}</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">additional_dataset_args</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<p>Instanciate a new DeepProg Boosting instance.
The default parameters are defined in the config.py file</p>
<dl class="simple">
<dt>Parameters:</dt><dd><dl class="field-list simple">
<dt class="field-odd">nb_it</dt>
<dd class="field-odd"><p>Number of models to construct</p>
</dd>
<dt class="field-even">do_KM_plot</dt>
<dd class="field-even"><p>Plot Kaplan-Meier (default: True)</p>
</dd>
<dt class="field-odd">distribute</dt>
<dd class="field-odd"><p>Distribute DeepProg using ray (default: False)</p>
</dd>
<dt class="field-even">nb_threads</dt>
<dd class="field-even"><p>Number of python threads to use to compute parallel Cox-PH</p>
</dd>
<dt class="field-odd">class_selection</dt>
<dd class="field-odd"><p>Consensus score to agglomerate DeepProg Instance {‘mean’, ‘max’, ‘weighted_mean’, ‘weighted_max’} (default: ‘mean’)</p>
</dd>
<dt class="field-even">model_thres</dt>
<dd class="field-even"><p>Cox-PH p-value threshold to reject a model for DeepProg Boosting module</p>
</dd>
<dt class="field-odd">verbose</dt>
<dd class="field-odd"><p>Verobosity (Default: True)</p>
</dd>
<dt class="field-even">seed</dt>
<dd class="field-even"><p>Seed defining the random split of the training dataset (Default: None).</p>
</dd>
<dt class="field-odd">project_name</dt>
<dd class="field-odd"><p>Project name used to save files</p>
</dd>
<dt class="field-even">use_autoencoders</dt>
<dd class="field-even"><p>Use autoencoder steps to embed the data (default: True)</p>
</dd>
<dt class="field-odd">feature_surv_analysis</dt>
<dd class="field-odd"><p>Use individual survival feature detection to filter out features (default: True)</p>
</dd>
<dt class="field-even">split_n_fold</dt>
<dd class="field-even"><p>For each instance, the original dataset is split in folds and one fold is left</p>
</dd>
<dt class="field-odd">path_results</dt>
<dd class="field-odd"><p>Path to create a result folder</p>
</dd>
<dt class="field-even">nb_clusters</dt>
<dd class="field-even"><p>Number of clusters to use</p>
</dd>
<dt class="field-odd">epochs</dt>
<dd class="field-odd"><p>Number of epochs</p>
</dd>
<dt class="field-even">normalization</dt>
<dd class="field-even"><p>Normalisation procedure to use. See config.py file for details</p>
</dd>
<dt class="field-odd">nb_selected_features</dt>
<dd class="field-odd"><p>Number of top features selected for classification</p>
</dd>
<dt class="field-even">cluster_method</dt>
<dd class="field-even"><p>Clustering method. possible choice: [‘mixture’, ‘kmeans’, ‘coxPH’] or class instance having fit and fit_proba attributes</p>
</dd>
<dt class="field-odd">pvalue_thres</dt>
<dd class="field-odd"><p>Threshold for survival significance to set a node as valid</p>
</dd>
<dt class="field-even">classification_method</dt>
<dd class="field-even"><p>Possible choice: {‘ALL_FEATURES’, ‘SURVIVAL_FEATURES’} (default: ‘ALL_FEATURES’)</p>
</dd>
<dt class="field-odd">new_dim</dt>
<dd class="field-odd"><p>Size of the new embedding</p>
</dd>
<dt class="field-even">training_tsv</dt>
<dd class="field-even"><p>Input matrix files</p>
</dd>
<dt class="field-odd">survival_tsv</dt>
<dd class="field-odd"><p>Input surival file</p>
</dd>
<dt class="field-even">survival_flag</dt>
<dd class="field-even"><p>Survival flag to use</p>
</dd>
<dt class="field-odd">path_data</dt>
<dd class="field-odd"><p>Path of the input file</p>
</dd>
<dt class="field-even">level_dims_in</dt>
<dd class="field-even"><p>Autoencoder node layers before the middle layer (default: [])</p>
</dd>
<dt class="field-odd">level_dims_out</dt>
<dd class="field-odd"><p>Autoencoder node layers after the middle layer (default: [])</p>
</dd>
<dt class="field-even">loss</dt>
<dd class="field-even"><p>Loss function to minimize (default: ‘binary_crossentropy’)</p>
</dd>
<dt class="field-odd">optimizer</dt>
<dd class="field-odd"><p>Optimizer (default: adam)</p>
</dd>
<dt class="field-even">act_reg</dt>
<dd class="field-even"><p>L2 Regularization constant on the node activity (default: False)</p>
</dd>
<dt class="field-odd">w_reg</dt>
<dd class="field-odd"><p>L1 Regularization constant on the weight (default: False)</p>
</dd>
<dt class="field-even">dropout</dt>
<dd class="field-even"><p>Percentage of edges being dropout at each training iteration (None for no dropout) (default: 0.5)</p>
</dd>
<dt class="field-odd">data_split</dt>
<dd class="field-odd"><p>Fraction of the dataset to be used as test set when building the autoencoder (default: None)</p>
</dd>
<dt class="field-even">node_selection</dt>
<dd class="field-even"><p>possible choice: {‘Cox-PH’, ‘C-index’} (default: Cox-PH)</p>
</dd>
<dt class="field-odd">cindex_thres</dt>
<dd class="field-odd"><p>Valid if ‘c-index’ is chosen (default: 0.65)</p>
</dd>
<dt class="field-even">activation</dt>
<dd class="field-even"><p>Activation function (default: ‘tanh’)</p>
</dd>
<dt class="field-odd">clustering_omics</dt>
<dd class="field-odd"><p>Which omics to use for clustering. If empty, then all the available omics will be used (default [] => all)</p>
</dd>
<dt class="field-even">path_to_save_model</dt>
<dd class="field-even"><p>path to save the model</p>
</dd>
<dt class="field-odd">metadata_usage</dt>
<dd class="field-odd"><p>Meta data usage with survival models (if metadata_tsv provided as argument to the dataset). Possible choice are [None, False, ‘labels’, ‘new-features’, ‘all’, True] (True is the same as all)</p>
</dd>
<dt class="field-even">subset_training_with_meta</dt>
<dd class="field-even"><p>Use a metadata key-value dict {meta_key:value} to subset the training sets</p>
</dd>
<dt class="field-odd">alternative_embedding</dt>
<dd class="field-odd"><p>alternative external embedding to use instead of building autoencoders (default None)</p>
</dd>
<dt class="field-even">kwargs_alternative_embedding</dt>
<dd class="field-even"><p>parameters for external embedding fitting</p>
</dd>
</dl>
</dd>
</dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_full_dataset">
<code class="sig-name descname">collect_cindex_for_full_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_cindex_for_full_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_full_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_test_dataset">
<code class="sig-name descname">collect_cindex_for_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_cindex_for_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_test_fold">
<code class="sig-name descname">collect_cindex_for_test_fold</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_cindex_for_test_fold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_test_fold" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_training_dataset">
<code class="sig-name descname">collect_cindex_for_training_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_cindex_for_training_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_cindex_for_training_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_number_of_features_per_omic">
<code class="sig-name descname">collect_number_of_features_per_omic</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_number_of_features_per_omic"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_number_of_features_per_omic" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_full_dataset">
<code class="sig-name descname">collect_pvalue_on_full_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_pvalue_on_full_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_full_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_test_dataset">
<code class="sig-name descname">collect_pvalue_on_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_pvalue_on_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_test_fold">
<code class="sig-name descname">collect_pvalue_on_test_fold</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_pvalue_on_test_fold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_test_fold" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_training_dataset">
<code class="sig-name descname">collect_pvalue_on_training_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.collect_pvalue_on_training_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.collect_pvalue_on_training_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_for_full_dataset">
<code class="sig-name descname">compute_c_indexes_for_full_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_c_indexes_for_full_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_for_full_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_for_test_dataset">
<code class="sig-name descname">compute_c_indexes_for_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_c_indexes_for_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_for_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>return c-index using labels as predicat</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_multiple_for_test_dataset">
<code class="sig-name descname">compute_c_indexes_multiple_for_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_c_indexes_multiple_for_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_c_indexes_multiple_for_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>Not Functionnal !</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_clusters_consistency_for_full_labels">
<code class="sig-name descname">compute_clusters_consistency_for_full_labels</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_clusters_consistency_for_full_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_clusters_consistency_for_full_labels" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_clusters_consistency_for_test_labels">
<code class="sig-name descname">compute_clusters_consistency_for_test_labels</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_clusters_consistency_for_test_labels"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_clusters_consistency_for_test_labels" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_feature_scores_per_cluster">
<code class="sig-name descname">compute_feature_scores_per_cluster</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">pval_thres</span><span class="o">=</span><span class="default_value">0.001</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_feature_scores_per_cluster"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_feature_scores_per_cluster" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_pvalue_for_merged_test_fold">
<code class="sig-name descname">compute_pvalue_for_merged_test_fold</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_pvalue_for_merged_test_fold"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_pvalue_for_merged_test_fold" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.compute_survival_feature_scores_per_cluster">
<code class="sig-name descname">compute_survival_feature_scores_per_cluster</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">pval_thres</span><span class="o">=</span><span class="default_value">0.001</span></em>, <em class="sig-param"><span class="n">use_meta</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.compute_survival_feature_scores_per_cluster"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.compute_survival_feature_scores_per_cluster" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.evalutate_cluster_performance">
<code class="sig-name descname">evalutate_cluster_performance</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.evalutate_cluster_performance"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.evalutate_cluster_performance" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.fit">
<code class="sig-name descname">fit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">debug</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">pretrained_labels_files</span><span class="o">=</span><span class="default_value">[]</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.fit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.fit" title="Permalink to this definition">¶</a></dt>
<dd><p>if pretrained_labels_files, is given, the models are constructed using these labels</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.fit_on_pretrained_label_file">
<code class="sig-name descname">fit_on_pretrained_label_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">labels_files</span><span class="o">=</span><span class="default_value">[]</span></em>, <em class="sig-param"><span class="n">labels_files_folder</span><span class="o">=</span><span class="default_value">''</span></em>, <em class="sig-param"><span class="n">file_name_regex</span><span class="o">=</span><span class="default_value">'*.tsv'</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">debug</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.fit_on_pretrained_label_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.fit_on_pretrained_label_file" title="Permalink to this definition">¶</a></dt>
<dd><p>fit a deepprog simdeep models without training autoencoders but using isntead ID->labels files (one for each model instance)</p>
</dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.load_new_test_dataset">
<code class="sig-name descname">load_new_test_dataset</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">tsv_dict</span></em>, <em class="sig-param"><span class="n">fname_key</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">path_survival_file</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">normalization</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">debug</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">verbose</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">survival_flag</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">metadata_file</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.load_new_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.load_new_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.partial_fit">
<code class="sig-name descname">partial_fit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">debug</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.partial_fit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.partial_fit" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.plot_supervised_kernel_for_test_sets">
<code class="sig-name descname">plot_supervised_kernel_for_test_sets</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.plot_supervised_kernel_for_test_sets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.plot_supervised_kernel_for_test_sets" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.plot_supervised_predicted_labels_for_test_sets">
<code class="sig-name descname">plot_supervised_predicted_labels_for_test_sets</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">define_as_main_kernel</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">use_main_kernel</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.plot_supervised_predicted_labels_for_test_sets"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.plot_supervised_predicted_labels_for_test_sets" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.predict_labels_on_full_dataset">
<code class="sig-name descname">predict_labels_on_full_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.predict_labels_on_full_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.predict_labels_on_full_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.predict_labels_on_test_dataset">
<code class="sig-name descname">predict_labels_on_test_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.predict_labels_on_test_dataset"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.predict_labels_on_test_dataset" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.save_cv_models_classes">
<code class="sig-name descname">save_cv_models_classes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_results</span><span class="o">=</span><span class="default_value">''</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.save_cv_models_classes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.save_cv_models_classes" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.save_models_classes">
<code class="sig-name descname">save_models_classes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_results</span><span class="o">=</span><span class="default_value">''</span></em>, <em class="sig-param"><span class="n">use_cv_labels</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">use_test_labels</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.save_models_classes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.save_models_classes" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.save_test_models_classes">
<code class="sig-name descname">save_test_models_classes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_results</span><span class="o">=</span><span class="default_value">''</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.save_test_models_classes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.save_test_models_classes" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.write_feature_score_per_cluster">
<code class="sig-name descname">write_feature_score_per_cluster</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.write_feature_score_per_cluster"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.write_feature_score_per_cluster" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.simdeep_boosting.SimDeepBoosting.write_logs">
<code class="sig-name descname">write_logs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_boosting.html#SimDeepBoosting.write_logs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_boosting.SimDeepBoosting.write_logs" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
</div>
<div class="section" id="module-simdeep.simdeep_distributed">
<span id="simdeep-simdeep-distributed-module"></span><h2>simdeep.simdeep_distributed module<a class="headerlink" href="#module-simdeep.simdeep_distributed" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="module-simdeep.simdeep_multiple_dataset">
<span id="simdeep-simdeep-multiple-dataset-module"></span><h2>simdeep.simdeep_multiple_dataset module<a class="headerlink" href="#module-simdeep.simdeep_multiple_dataset" title="Permalink to this headline">¶</a></h2>
<dl class="py class">
<dt id="simdeep.simdeep_multiple_dataset.SimDeepMultiple">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.simdeep_multiple_dataset.</code><code class="sig-name descname">SimDeepMultiple</code><a class="reference internal" href="../_modules/simdeep/simdeep_multiple_dataset.html#SimDeepMultiple"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_multiple_dataset.SimDeepMultiple" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference internal" href="#simdeep.simdeep_analysis.SimDeep" title="simdeep.simdeep_analysis.SimDeep"><code class="xref py py-class docutils literal notranslate"><span class="pre">simdeep.simdeep_analysis.SimDeep</span></code></a></p>
</dd></dl>
</div>
<div class="section" id="module-simdeep.simdeep_utils">
<span id="simdeep-simdeep-utils-module"></span><h2>simdeep.simdeep_utils module<a class="headerlink" href="#module-simdeep.simdeep_utils" title="Permalink to this headline">¶</a></h2>
<dl class="py function">
<dt id="simdeep.simdeep_utils.feature_selection_usage_type">
<code class="sig-prename descclassname">simdeep.simdeep_utils.</code><code class="sig-name descname">feature_selection_usage_type</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">value</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_utils.html#feature_selection_usage_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_utils.feature_selection_usage_type" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.simdeep_utils.load_labels_file">
<code class="sig-prename descclassname">simdeep.simdeep_utils.</code><code class="sig-name descname">load_labels_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_labels</span></em>, <em class="sig-param"><span class="n">sep</span><span class="o">=</span><span class="default_value">'\t'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_utils.html#load_labels_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_utils.load_labels_file" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.simdeep_utils.load_model">
<code class="sig-prename descclassname">simdeep.simdeep_utils.</code><code class="sig-name descname">load_model</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">project_name</span></em>, <em class="sig-param"><span class="n">path_model</span><span class="o">=</span><span class="default_value">'./'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_utils.html#load_model"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_utils.load_model" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.simdeep_utils.metadata_usage_type">
<code class="sig-prename descclassname">simdeep.simdeep_utils.</code><code class="sig-name descname">metadata_usage_type</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">value</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_utils.html#metadata_usage_type"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_utils.metadata_usage_type" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.simdeep_utils.save_model">
<code class="sig-prename descclassname">simdeep.simdeep_utils.</code><code class="sig-name descname">save_model</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">boosting</span></em>, <em class="sig-param"><span class="n">path_to_save_model</span><span class="o">=</span><span class="default_value">'./'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/simdeep_utils.html#save_model"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.simdeep_utils.save_model" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</div>
<div class="section" id="module-simdeep.survival_utils">
<span id="simdeep-survival-utils-module"></span><h2>simdeep.survival_utils module<a class="headerlink" href="#module-simdeep.survival_utils" title="Permalink to this headline">¶</a></h2>
<dl class="py class">
<dt id="simdeep.survival_utils.CorrelationReducer">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">CorrelationReducer</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">distance</span><span class="o">=</span><span class="default_value">'correlation'</span></em>, <em class="sig-param"><span class="n">threshold</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#CorrelationReducer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.CorrelationReducer" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="py method">
<dt id="simdeep.survival_utils.CorrelationReducer.fit">
<code class="sig-name descname">fit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#CorrelationReducer.fit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.CorrelationReducer.fit" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.survival_utils.CorrelationReducer.fit_transform">
<code class="sig-name descname">fit_transform</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#CorrelationReducer.fit_transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.CorrelationReducer.fit_transform" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.survival_utils.CorrelationReducer.transform">
<code class="sig-name descname">transform</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#CorrelationReducer.transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.CorrelationReducer.transform" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt id="simdeep.survival_utils.MadScaler">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">MadScaler</code><a class="reference internal" href="../_modules/simdeep/survival_utils.html#MadScaler"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.MadScaler" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="py method">
<dt id="simdeep.survival_utils.MadScaler.fit_transform">
<code class="sig-name descname">fit_transform</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">X</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#MadScaler.fit_transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.MadScaler.fit_transform" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt id="simdeep.survival_utils.RankCorrNorm">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">RankCorrNorm</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#RankCorrNorm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.RankCorrNorm" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
</dd></dl>
<dl class="py class">
<dt id="simdeep.survival_utils.RankNorm">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">RankNorm</code><a class="reference internal" href="../_modules/simdeep/survival_utils.html#RankNorm"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.RankNorm" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="py method">
<dt id="simdeep.survival_utils.RankNorm.fit_transform">
<code class="sig-name descname">fit_transform</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">X</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#RankNorm.fit_transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.RankNorm.fit_transform" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt id="simdeep.survival_utils.SampleReducer">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">SampleReducer</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">perc_sample_to_keep</span><span class="o">=</span><span class="default_value">0.9</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#SampleReducer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.SampleReducer" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="py method">
<dt id="simdeep.survival_utils.SampleReducer.sample_to_keep">
<code class="sig-name descname">sample_to_keep</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">datasets</span></em>, <em class="sig-param"><span class="n">index</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#SampleReducer.sample_to_keep"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.SampleReducer.sample_to_keep" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt id="simdeep.survival_utils.VarianceReducer">
<em class="property">class </em><code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">VarianceReducer</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">nb_features</span><span class="o">=</span><span class="default_value">200</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#VarianceReducer"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.VarianceReducer" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="py method">
<dt id="simdeep.survival_utils.VarianceReducer.fit">
<code class="sig-name descname">fit</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#VarianceReducer.fit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.VarianceReducer.fit" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.survival_utils.VarianceReducer.fit_transform">
<code class="sig-name descname">fit_transform</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#VarianceReducer.fit_transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.VarianceReducer.fit_transform" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt id="simdeep.survival_utils.VarianceReducer.transform">
<code class="sig-name descname">transform</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">dataset</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#VarianceReducer.transform"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.VarianceReducer.transform" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.convert_metadata_frame_to_matrix">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">convert_metadata_frame_to_matrix</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">frame</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#convert_metadata_frame_to_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.convert_metadata_frame_to_matrix" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.load_data_from_tsv">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">load_data_from_tsv</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">use_transpose</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="o">**</span><span class="n">kwargs</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#load_data_from_tsv"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.load_data_from_tsv" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.load_entrezID_to_ensg">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">load_entrezID_to_ensg</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#load_entrezID_to_ensg"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.load_entrezID_to_ensg" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.load_survival_file">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">load_survival_file</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">f_name</span></em>, <em class="sig-param"><span class="n">path_data</span><span class="o">=</span><span class="default_value">'/home/oliver/code/SimDeep/simdeep/../examples/data/'</span></em>, <em class="sig-param"><span class="n">sep</span><span class="o">=</span><span class="default_value">'\t'</span></em>, <em class="sig-param"><span class="n">survival_flag</span><span class="o">=</span><span class="default_value">{'event': 'recurrence', 'patient_id': 'barcode', 'survival': 'days'}</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#load_survival_file"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.load_survival_file" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.return_intersection_indexes">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">return_intersection_indexes</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">ids_1</span></em>, <em class="sig-param"><span class="n">ids_2</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#return_intersection_indexes"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.return_intersection_indexes" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.save_matrix">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">save_matrix</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">matrix</span></em>, <em class="sig-param"><span class="n">feature_array</span></em>, <em class="sig-param"><span class="n">sample_array</span></em>, <em class="sig-param"><span class="n">path_folder</span></em>, <em class="sig-param"><span class="n">project_name</span></em>, <em class="sig-param"><span class="n">key</span><span class="o">=</span><span class="default_value">''</span></em>, <em class="sig-param"><span class="n">sep</span><span class="o">=</span><span class="default_value">'\t'</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#save_matrix"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.save_matrix" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.select_best_classif_params">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">select_best_classif_params</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">clf</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#select_best_classif_params"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.select_best_classif_params" title="Permalink to this definition">¶</a></dt>
<dd><p>select best classifier parameters based uniquely
on test errors</p>
</dd></dl>
<dl class="py function">
<dt id="simdeep.survival_utils.translate_index">
<code class="sig-prename descclassname">simdeep.survival_utils.</code><code class="sig-name descname">translate_index</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">original_ids</span></em>, <em class="sig-param"><span class="n">new_ids</span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/simdeep/survival_utils.html#translate_index"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#simdeep.survival_utils.translate_index" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</div>
<div class="section" id="module-simdeep">
<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-simdeep" title="Permalink to this headline">¶</a></h2>
</div>
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Datasets
Models
