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<section id="module-histocartography.ml.layers.pna_layer">
<span id="histocartography-ml-layers-pna-layer-module"></span><h1>histocartography.ml.layers.pna_layer module<a class="headerlink" href="#module-histocartography.ml.layers.pna_layer" title="Permalink to this headline">¶</a></h1>
<p>PNA: Principal Neighbourhood Aggregation
Gabriele Corso, Luca Cavalleri, Dominique Beaini, Pietro Lio, Petar Velickovic
<a class="reference external" href="https://arxiv.org/abs/2004.05718">https://arxiv.org/abs/2004.05718</a></p>
<section id="summary">
<h2>Summary<a class="headerlink" href="#summary" title="Permalink to this headline">¶</a></h2>
<p>Classes:</p>
<table class="longtable docutils align-default">
<colgroup>
<col style="width: 10%" />
<col style="width: 90%" />
</colgroup>
<tbody>
<tr class="row-odd"><td><p><a class="reference internal" href="#histocartography.ml.layers.pna_layer.PNALayer" title="histocartography.ml.layers.pna_layer.PNALayer"><code class="xref py py-obj docutils literal notranslate"><span class="pre">PNALayer</span></code></a></p></td>
<td><p></p></td>
</tr>
<tr class="row-even"><td><p><a class="reference internal" href="#histocartography.ml.layers.pna_layer.PNATower" title="histocartography.ml.layers.pna_layer.PNATower"><code class="xref py py-obj docutils literal notranslate"><span class="pre">PNATower</span></code></a></p></td>
<td><p></p></td>
</tr>
</tbody>
</table>
<dl class="py class">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNALayer">
<em class="property"><span class="pre">class</span> </em><span class="sig-name descname"><span class="pre">PNALayer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node_dim</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out_dim</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregators</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">'mean</span> <span class="pre">max</span> <span class="pre">min</span> <span class="pre">std'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scalers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">'identity</span> <span class="pre">amplification</span> <span class="pre">attenuation'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">avg_d</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dropout</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">float</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_norm</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_norm</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">towers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pretrans_layers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">posttrans_layers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">divide_input</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">residual</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNALayer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNALayer" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">torch.nn.modules.module.Module</span></code></p>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNALayer.__init__">
<span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">node_dim</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out_dim</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregators</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">'mean</span> <span class="pre">max</span> <span class="pre">min</span> <span class="pre">std'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scalers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">str</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">'identity</span> <span class="pre">amplification</span> <span class="pre">attenuation'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">avg_d</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">4</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dropout</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">float</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_norm</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_norm</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">towers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pretrans_layers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">posttrans_layers</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">divide_input</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">residual</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">bool</span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNALayer.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNALayer.__init__" title="Permalink to this definition">¶</a></dt>
<dd><p>PNA layer constructor.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>node_dim</strong> (<em>int</em>) – Input dimension of each node.</p></li>
<li><p><strong>out_dim</strong> (<em>int</em>) – Output dimension of each node.</p></li>
<li><p><strong>aggregators</strong> (<em>str</em>) – Set of aggregation function identifiers. Default to “mean max min std”.</p></li>
<li><p><strong>scalers</strong> (<em>str</em>) – Set of scaling functions identifiers. Default to “identity amplification attenuation”.</p></li>
<li><p><strong>avg_d</strong> (<em>int</em>) – Average degree of nodes in the training set, used by scalers to normalize. Default to 5.</p></li>
<li><p><strong>dropout</strong> (<em>float</em>) – Dropout used. Default to 0.</p></li>
<li><p><strong>graph_norm</strong> (<em>bool</em>) – Whether to use graph normalisation. Default to False.</p></li>
<li><p><strong>batch_norm</strong> (<em>bool</em>) – Whether to use batch normalisation. Default to False.</p></li>
<li><p><strong>towers</strong> – Number of towers to use. Default to 1.</p></li>
<li><p><strong>pretrans_layers</strong> – Number of layers in the transformation before the aggregation. Default to 1.</p></li>
<li><p><strong>posttrans_layers</strong> – Number of layers in the transformation after the aggregation. Default to 1.</p></li>
<li><p><strong>divide_input</strong> – Whether the input features should be split between towers or not. Default to True.</p></li>
<li><p><strong>residual</strong> – Whether to add a residual connection. Default to True.</p></li>
<li><p><strong>verbose</strong> (<em>bool</em>) – Verbosity. Default to False.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNALayer.forward">
<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">g</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">h</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNALayer.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNALayer.forward" title="Permalink to this definition">¶</a></dt>
<dd><p>Defines the computation performed at every call.</p>
<p>Should be overridden by all subclasses.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Although the recipe for forward pass needs to be defined within
this function, one should call the <code class="xref py py-class docutils literal notranslate"><span class="pre">Module</span></code> instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.</p>
</div>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNALayer.set_rlp">
<span class="sig-name descname"><span class="pre">set_rlp</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">with_rlp</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNALayer.set_rlp"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNALayer.set_rlp" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNATower">
<em class="property"><span class="pre">class</span> </em><span class="sig-name descname"><span class="pre">PNATower</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">in_dim</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out_dim</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dropout</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">graph_norm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_norm</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregators</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">scalers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">avg_d</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pretrans_layers</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">posttrans_layers</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNATower"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNATower" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">torch.nn.modules.module.Module</span></code></p>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNATower.pretrans_edges">
<span class="sig-name descname"><span class="pre">pretrans_edges</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">edges</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNATower.pretrans_edges"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNATower.pretrans_edges" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNATower.message_func">
<span class="sig-name descname"><span class="pre">message_func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">edges</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNATower.message_func"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNATower.message_func" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNATower.reduce_func">
<span class="sig-name descname"><span class="pre">reduce_func</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nodes</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNATower.reduce_func"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNATower.reduce_func" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNATower.posttrans_nodes">
<span class="sig-name descname"><span class="pre">posttrans_nodes</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">nodes</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNATower.posttrans_nodes"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNATower.posttrans_nodes" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="histocartography.ml.layers.pna_layer.PNATower.forward">
<span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">g</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">h</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/histocartography/ml/layers/pna_layer.html#PNATower.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#histocartography.ml.layers.pna_layer.PNATower.forward" title="Permalink to this definition">¶</a></dt>
<dd><p>Defines the computation performed at every call.</p>
<p>Should be overridden by all subclasses.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Although the recipe for forward pass needs to be defined within
this function, one should call the <code class="xref py py-class docutils literal notranslate"><span class="pre">Module</span></code> instance afterwards
instead of this since the former takes care of running the
registered hooks while the latter silently ignores them.</p>
</div>
</dd></dl>
</dd></dl>
</section>
<section id="reference">
<h2>Reference<a class="headerlink" href="#reference" title="Permalink to this headline">¶</a></h2>
<p>If you use <cite>histocartography</cite> in your projects, please cite the following:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="nd">@inproceedings</span><span class="p">{</span><span class="n">pati2021</span><span class="p">,</span>
<span class="n">title</span> <span class="o">=</span> <span class="p">{</span><span class="n">Hierarchical</span> <span class="n">Graph</span> <span class="n">Representations</span> <span class="k">for</span> <span class="n">Digital</span> <span class="n">Pathology</span><span class="p">},</span>
<span class="n">author</span> <span class="o">=</span> <span class="p">{</span><span class="n">Pushpak</span> <span class="n">Pati</span><span class="p">,</span> <span class="n">Guillaume</span> <span class="n">Jaume</span><span class="p">,</span> <span class="n">Antonio</span> <span class="n">Foncubierta</span><span class="p">,</span> <span class="n">Florinda</span> <span class="n">Feroce</span><span class="p">,</span> <span class="n">Anna</span> <span class="n">Maria</span> <span class="n">Anniciello</span><span class="p">,</span> <span class="n">Giosuè</span> <span class="n">Scognamiglio</span><span class="p">,</span> <span class="n">Nadia</span> <span class="n">Brancati</span><span class="p">,</span> <span class="n">Maryse</span> <span class="n">Fiche</span><span class="p">,</span> <span class="n">Estelle</span> <span class="n">Dubruc</span><span class="p">,</span> <span class="n">Daniel</span> <span class="n">Riccio</span><span class="p">,</span> <span class="n">Maurizio</span> <span class="n">Di</span> <span class="n">Bonito</span><span class="p">,</span> <span class="n">Giuseppe</span> <span class="n">De</span> <span class="n">Pietro</span><span class="p">,</span> <span class="n">Gerardo</span> <span class="n">Botti</span><span class="p">,</span> <span class="n">Jean</span><span class="o">-</span><span class="n">Philippe</span> <span class="n">Thiran</span><span class="p">,</span> <span class="n">Maria</span> <span class="n">Frucci</span><span class="p">,</span> <span class="n">Orcun</span> <span class="n">Goksel</span><span class="p">,</span> <span class="n">Maria</span> <span class="n">Gabrani</span><span class="p">},</span>
<span class="n">booktitle</span> <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">arxiv</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">pdf</span><span class="o">/</span><span class="mf">2102.11057</span><span class="p">},</span>
<span class="n">year</span> <span class="o">=</span> <span class="p">{</span><span class="mi">2021</span><span class="p">}</span>
<span class="p">}</span>
</pre></div>
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