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  <section id="slideflow-mil">
<span id="mil-api"></span><h1>slideflow.mil<a class="headerlink" href="#slideflow-mil" title="Permalink to this heading">¶</a></h1>
<p>This submodule contains tools for multiple-instance learning (MIL) model training and evaluation. See <a class="reference internal" href="../mil/#mil"><span class="std std-ref">Multiple-Instance Learning (MIL)</span></a> for more information. A summary of the API is given below.</p>
<dl class="simple">
<dt><strong>Training:</strong></dt><dd><ul class="simple">
<li><p><a class="reference internal" href="#slideflow.mil.train_mil" title="slideflow.mil.train_mil"><code class="xref py py-func docutils literal notranslate"><span class="pre">train_mil()</span></code></a>: Train an MIL model, using an MIL configuration, Datasets, and a directory of bags.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.build_fastai_learner" title="slideflow.mil.build_fastai_learner"><code class="xref py py-func docutils literal notranslate"><span class="pre">build_fastai_learner()</span></code></a>: Build and return the FastAI Learner, but do not execute training. Useful for customizing training.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.build_multimodal_learner" title="slideflow.mil.build_multimodal_learner"><code class="xref py py-func docutils literal notranslate"><span class="pre">build_multimodal_learner()</span></code></a>: Build and return a FastAI Learner designed for multi-modal/multi-magnification input.</p></li>
</ul>
</dd>
<dt><strong>Evaluation/Inference:</strong></dt><dd><ul class="simple">
<li><p><a class="reference internal" href="#slideflow.mil.eval_mil" title="slideflow.mil.eval_mil"><code class="xref py py-func docutils literal notranslate"><span class="pre">eval_mil()</span></code></a>: Evaluate an MIL model using a path to a saved model, a Dataset, and path to bags. Generates metrics.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.predict_mil" title="slideflow.mil.predict_mil"><code class="xref py py-func docutils literal notranslate"><span class="pre">predict_mil()</span></code></a>: Generate predictions from an MIL model and saved bags. Returns a pandas dataframe.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.predict_multimodal_mil" title="slideflow.mil.predict_multimodal_mil"><code class="xref py py-func docutils literal notranslate"><span class="pre">predict_multimodal_mil()</span></code></a>: Generate predictions from a multimodal MIL model. Returns a dataframe.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.predict_slide" title="slideflow.mil.predict_slide"><code class="xref py py-func docutils literal notranslate"><span class="pre">predict_slide()</span></code></a>: Generate MIL predictions for a single slide. Returns a 2D array of predictions and attention.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.predict_from_bags" title="slideflow.mil.predict_from_bags"><code class="xref py py-func docutils literal notranslate"><span class="pre">predict_from_bags()</span></code></a>: Low-level interface for generating predictions from a loaded MIL model and pre-loaded bag Tensors.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.predict_from_multimodal_bags" title="slideflow.mil.predict_from_multimodal_bags"><code class="xref py py-func docutils literal notranslate"><span class="pre">predict_from_multimodal_bags()</span></code></a>: Low-level interface for generating multimodal predictions from a loaded MIL model and bag Tensors.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.get_mil_tile_predictions" title="slideflow.mil.get_mil_tile_predictions"><code class="xref py py-func docutils literal notranslate"><span class="pre">get_mil_tile_predictions()</span></code></a>: Get tile-level predictions and attention from a saved MIL model for a given Dataset and saved bags.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.generate_attention_heatmaps" title="slideflow.mil.generate_attention_heatmaps"><code class="xref py py-func docutils literal notranslate"><span class="pre">generate_attention_heatmaps()</span></code></a>: Generate and save attention heatmaps.</p></li>
<li><p><a class="reference internal" href="#slideflow.mil.generate_mil_features" title="slideflow.mil.generate_mil_features"><code class="xref py py-func docutils literal notranslate"><span class="pre">generate_mil_features()</span></code></a>: Get last-layer activations from an MIL model. Returns an MILFeatures object.</p></li>
</ul>
</dd>
</dl>
<section id="main-functions">
<h2>Main functions<a class="headerlink" href="#main-functions" title="Permalink to this heading">¶</a></h2>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.mil_config">
<span class="sig-name descname"><span class="pre">mil_config</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">trainer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'fastai'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/mil/_params/#mil_config"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.mil_config" title="Permalink to this definition">¶</a></dt>
<dd><p>Create a multiple-instance learning (MIL) training configuration.</p>
<p>All models by default are trained with the FastAI trainer. Additional
trainers and additional models can be installed with <code class="docutils literal notranslate"><span class="pre">slideflow-extras</span></code>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>Callable</em>) – Either the name of a model, or a custom torch
module. Valid model names include <code class="docutils literal notranslate"><span class="pre">&quot;attention_mil&quot;</span></code>,
<code class="docutils literal notranslate"><span class="pre">&quot;transmil&quot;</span></code>, and <code class="docutils literal notranslate"><span class="pre">&quot;bistro.transformer&quot;</span></code>.</p></li>
<li><p><strong>trainer</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Type of MIL trainer to use. Only ‘fastai’ is available,
unless additional trainers are installed.</p></li>
<li><p><strong>**kwargs</strong> – All additional keyword arguments are passed to
<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a></p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.train_mil">
<span class="sig-name descname"><span class="pre">train_mil</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">train_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">val_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mil'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_label</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Learner</span></span></span><a class="reference internal" href="../_modules/slideflow/mil/train/#train_mil"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.train_mil" title="Permalink to this definition">¶</a></dt>
<dd><p>Train a multiple-instance learning (MIL) model.</p>
<p>This high-level trainer facilitates training from a given MIL configuration,
using Datasets as input and with input features taken from a given directory
of bags.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Trainer and model configuration.</p></li>
<li><p><strong>train_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Training dataset.</p></li>
<li><p><strong>val_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Validation dataset.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Outcome column (annotation header) from which to
derive category labels.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Either a path to directory with *.pt files, or a list
of paths to individual *.pt files. Each file should contain
exported feature vectors, with each file containing all tile
features for one patient.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to save model and results.</p></li>
<li><p><strong>exp_label</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Experiment label, used for naming the subdirectory
in the <code class="docutils literal notranslate"><span class="pre">{project</span> <span class="pre">root}/mil</span></code> folder, where training history
and the model will be saved.</p></li>
<li><p><strong>attention_heatmaps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Generate attention heatmaps for slides.
Not available for multi-modal MIL models. Defaults to False.</p></li>
<li><p><strong>interpolation</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Interpolation strategy for smoothing
attention heatmaps. Defaults to ‘bicubic’.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Matplotlib colormap for heatmap. Can be any
valid matplotlib colormap. Defaults to ‘inferno’.</p></li>
<li><p><strong>norm</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Normalization strategy for assigning heatmap
values to colors. Either ‘two_slope’, or any other valid value
for the <code class="docutils literal notranslate"><span class="pre">norm</span></code> argument of <code class="docutils literal notranslate"><span class="pre">matplotlib.pyplot.imshow</span></code>.
If ‘two_slope’, normalizes values less than 0 and greater than 0
separately. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.build_fastai_learner">
<span class="sig-name descname"><span class="pre">build_fastai_learner</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">train_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">val_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mil'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_shape</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Learner</span></span></span><a class="reference internal" href="../_modules/slideflow/mil/train/#build_fastai_learner"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.build_fastai_learner" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a FastAI Learner for training an MIL model.</p>
<p>Does not execute training. Useful for customizing a Learner object
prior to training.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>train_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Training dataset.</p></li>
<li><p><strong>val_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Validation dataset.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Outcome column (annotation header) from which to
derive category labels.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – list of paths to individual *.pt files. Each file should
contain exported feature vectors, with each file containing all tile
features for one patient.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to save model and results.</p></li>
<li><p><strong>return_shape</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Return the input and output shapes of the model.
Defaults to False.</p></li>
<li><p><strong>exp_label</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Experiment label, used for naming the subdirectory
in the <code class="docutils literal notranslate"><span class="pre">outdir</span></code> folder, where training history
and the model will be saved.</p></li>
<li><p><strong>lr</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Learning rate, or maximum learning rate if
<code class="docutils literal notranslate"><span class="pre">fit_one_cycle=True</span></code>.</p></li>
<li><p><strong>epochs</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Maximum epochs.</p></li>
<li><p><strong>**kwargs</strong> – Additional keyword arguments to pass to the FastAI learner.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>fastai.learner.Learner, and optionally a tuple of input and output shapes
if <code class="docutils literal notranslate"><span class="pre">return_shape=True</span></code>.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.build_multimodal_learner">
<span class="sig-name descname"><span class="pre">build_multimodal_learner</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">train_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">val_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mil'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">return_shape</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Learner</span></span></span><a class="reference internal" href="../_modules/slideflow/mil/train/#build_multimodal_learner"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.build_multimodal_learner" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a multi-magnification FastAI Learner for training an MIL model.</p>
<p>Does not execute training. Useful for customizing a Learner object
prior to training.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>train_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Training dataset.</p></li>
<li><p><strong>val_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Validation dataset.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Outcome column (annotation header) from which to
derive category labels.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – List of bag directories containing *.pt files, one
directory for each mode.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to save model and results.</p></li>
<li><p><strong>return_shape</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Return the input and output shapes of the model.
Defaults to False.</p></li>
<li><p><strong>exp_label</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Experiment label, used for naming the subdirectory
in the <code class="docutils literal notranslate"><span class="pre">outdir</span></code> folder, where training history
and the model will be saved.</p></li>
<li><p><strong>lr</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Learning rate, or maximum learning rate if
<code class="docutils literal notranslate"><span class="pre">fit_one_cycle=True</span></code>.</p></li>
<li><p><strong>epochs</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Maximum epochs.</p></li>
<li><p><strong>**kwargs</strong> – Additional keyword arguments to pass to the FastAI learner.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>fastai.learner.Learner, and optionally a tuple of input and output shapes
if <code class="docutils literal notranslate"><span class="pre">return_shape=True</span></code>.</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.eval_mil">
<span class="sig-name descname"><span class="pre">eval_mil</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mil'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention_heatmaps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uq</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregation_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">heatmap_kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#eval_mil"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.eval_mil" title="Permalink to this definition">¶</a></dt>
<dd><p>Evaluate a multiple-instance learning model.</p>
<p>Saves results for the evaluation in the target folder, including
predictions (parquet format), attention (Numpy format for each slide),
and attention heatmaps (if <code class="docutils literal notranslate"><span class="pre">attention_heatmaps=True</span></code>).</p>
<p>Logs classifier metrics (AUROC and AP) to the console.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>weights</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to model weights to load.</p></li>
<li><p><strong>dataset</strong> (<em>sf.Dataset</em>) – Dataset to evaluation.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Outcomes.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Path to bags, or list of bag file paths.
Each bag should contain PyTorch array of features from all tiles in
a slide, with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Configuration for building model. If <code class="docutils literal notranslate"><span class="pre">weights</span></code> is a path to a
model directory, will attempt to read <code class="docutils literal notranslate"><span class="pre">mil_params.json</span></code> from this
location and load saved configuration. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path at which to save results.</p></li>
<li><p><strong>attention_heatmaps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Generate attention heatmaps for slides.
Not available for multi-modal MIL models. Defaults to False.</p></li>
<li><p><strong>interpolation</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Interpolation strategy for smoothing
attention heatmaps. Defaults to ‘bicubic’.</p></li>
<li><p><strong>aggregation_level</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Aggregation level for predictions.
Either ‘slide’ or ‘patient’. Defaults to None (uses the model
configuration).</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Matplotlib colormap for heatmap. Can be any
valid matplotlib colormap. Defaults to ‘inferno’.</p></li>
<li><p><strong>norm</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Normalization strategy for assigning heatmap
values to colors. Either ‘two_slope’, or any other valid value
for the <code class="docutils literal notranslate"><span class="pre">norm</span></code> argument of <code class="docutils literal notranslate"><span class="pre">matplotlib.pyplot.imshow</span></code>.
If ‘two_slope’, normalizes values less than 0 and greater than 0
separately. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.predict_mil">
<span class="sig-name descname"><span class="pre">predict_mil</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregation_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">DataFrame</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#predict_mil"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.predict_mil" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate predictions for a dataset from a saved MIL model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Model from which to generate predictions.</p></li>
<li><p><strong>dataset</strong> (<em>sf.Dataset</em>) – Dataset from which to generation predictions.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Outcomes.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Path to bags, or list of bag file paths.
Each bag should contain PyTorch array of features from all tiles in
a slide, with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Configuration for the MIL model. Required if model is a loaded <code class="docutils literal notranslate"><span class="pre">torch.nn.Module</span></code>.
Defaults to None.</p></li>
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to calculate attention scores. Defaults to False.</p></li>
<li><p><strong>uq</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to generate uncertainty estimates. Experimental. Defaults to False.</p></li>
<li><p><strong>aggregation_level</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Aggregation level for predictions. Either ‘slide’
or ‘patient’. Defaults to None.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Attention pooling strategy. Either ‘avg’
or ‘max’. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><p>Dataframe of predictions.</p>
<p>list(np.ndarray): Attention scores (if <code class="docutils literal notranslate"><span class="pre">attention=True</span></code>)</p>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>pd.DataFrame</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.predict_multimodal_mil">
<span class="sig-name descname"><span class="pre">predict_multimodal_mil</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregation_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">DataFrame</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#predict_multimodal_mil"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.predict_multimodal_mil" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate predictions for a dataset from a saved multimodal MIL model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Model from which to generate predictions.</p></li>
<li><p><strong>dataset</strong> (<em>sf.Dataset</em>) – Dataset from which to generation predictions.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Outcomes.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Path to bags, or list of bag file paths.
Each bag should contain PyTorch array of features from all tiles in
a slide, with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Configuration for the MIL model. Required if model is a loaded <code class="docutils literal notranslate"><span class="pre">torch.nn.Module</span></code>.
Defaults to None.</p></li>
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to calculate attention scores. Defaults to False.</p></li>
<li><p><strong>uq</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to generate uncertainty estimates. Defaults to False.</p></li>
<li><p><strong>aggregation_level</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Aggregation level for predictions. Either ‘slide’
or ‘patient’. Defaults to None.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Attention pooling strategy. Either ‘avg’
or ‘max’. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><p>Dataframe of predictions.</p>
<p>list(np.ndarray): Attention scores (if <code class="docutils literal notranslate"><span class="pre">attention=True</span></code>)</p>
</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>pd.DataFrame</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.predict_from_bags">
<span class="sig-name descname"><span class="pre">predict_from_bags</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">torch.nn.Module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention_pooling</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_lens</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apply_softmax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uq</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#predict_from_bags"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.predict_from_bags" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate MIL predictions for a list of bags.</p>
<p>Predictions are generated for each bag in the list one at a time, and not batched.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Loaded PyTorch MIL model.</p></li>
<li><p><strong>bags</strong> (<em>np.ndarray</em><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Bags to generate predictions for. Each bag
should contain PyTorch array of features from all tiles in a slide,
with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to calculate attention scores. Defaults to False.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Pooling strategy for attention scores.
Can be ‘avg’, ‘max’, or None. Defaults to None.</p></li>
<li><p><strong>use_lens</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to use the length of each bag as an additional
input to the model. Defaults to False.</p></li>
<li><p><strong>device</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Device on which to run inference. Defaults to None.</p></li>
<li><p><strong>apply_softmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to apply softmax to the model output. Defaults
to True for categorical outcomes, False for continuous outcomes.</p></li>
<li><p><strong>uq</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to generate uncertainty estimates. Defaults to False.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Predictions and attention scores.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray, List[np.ndarray]]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.predict_from_multimodal_bags">
<span class="sig-name descname"><span class="pre">predict_from_multimodal_bags</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">torch.nn.Module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention_pooling</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_lens</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apply_softmax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#predict_from_multimodal_bags"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.predict_from_multimodal_bags" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate multi-mag MIL predictions for a nested list of bags.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Loaded PyTorch MIL model.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em><em>)</em>) – Nested list of bags to generate predictions for.
Each bag should contain PyTorch array of features from all tiles in a slide,
with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to calculate attention scores. Defaults to False.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Pooling strategy for attention scores.
Can be ‘avg’, ‘max’, or None. Defaults to None.</p></li>
<li><p><strong>use_lens</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to use the length of each bag as an additional
input to the model. Defaults to False.</p></li>
<li><p><strong>device</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Device on which to run inference. Defaults to None.</p></li>
<li><p><strong>apply_softmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to apply softmax to the model output. Defaults
to True for categorical outcomes, False for continuous</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Predictions and attention scores.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray, List[List[np.ndarray]]]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.predict_slide">
<span class="sig-name descname"><span class="pre">predict_slide</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">slide</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference internal" href="../slide/#slideflow.slide.WSI" title="slideflow.slide.wsi.WSI"><span class="pre">WSI</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">extractor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">BaseFeatureExtractor</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">normalizer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../norm/#slideflow.norm.StainNormalizer" title="slideflow.norm.StainNormalizer"><span class="pre">StainNormalizer</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">native_normalizer</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">extractor_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#predict_slide"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.predict_slide" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate predictions (and attention) for a single slide.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to MIL model.</p></li>
<li><p><strong>slide</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to slide.</p></li>
<li><p><strong>extractor</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.BaseFeatureExtractor</span></code>, optional) – <p>Feature extractor. If not provided, will attempt to auto-detect
extractor from model.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>If the extractor has a stain normalizer, this will be used to
normalize the slide before extracting features.</p>
</div>
</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>normalizer</strong> (<code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.stain.StainNormalizer</span></code>, optional) – Stain normalizer. If not provided, will attempt to use stain
normalizer from extractor.</p></li>
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Configuration for building model. If None, will attempt to read
<code class="docutils literal notranslate"><span class="pre">mil_params.json</span></code> from the model directory and load saved
configuration. Defaults to None.</p></li>
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to return attention scores. Defaults to
False.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Attention pooling strategy. Either ‘avg’
or ‘max’. Defaults to None.</p></li>
<li><p><strong>native_normalizer</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether to use PyTorch/Tensorflow-native
stain normalization, if applicable. If False, will use the OpenCV/Numpy
implementations. Defaults to None, which auto-detects based on the
slide backend (False if libvips, True if cucim). This behavior is due
to performance issued when using native stain normalization with
libvips-compatible multiprocessing.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Predictions and attention scores.
Attention scores are None if <code class="docutils literal notranslate"><span class="pre">attention</span></code> is False. For single-channel attention,
this is a masked 2D array with the same shape as the slide grid (arranged as a
heatmap, with unused tiles masked). For multi-channel attention, this is a
masked 3D array with shape <code class="docutils literal notranslate"><span class="pre">(n_channels,</span> <span class="pre">X,</span> <span class="pre">Y)</span></code>.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray, Optional[np.ndarray]]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.get_mil_tile_predictions">
<span class="sig-name descname"><span class="pre">get_mil_tile_predictions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dest</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uq</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tile_batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">512</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#get_mil_tile_predictions"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.get_mil_tile_predictions" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate tile-level predictions for a MIL model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>weights</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to model weights to load.</p></li>
<li><p><strong>dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Dataset.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Path to bags, or list of bag file paths.
Each bag should contain PyTorch array of features from all tiles in
a slide, with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Configuration for building model. If <code class="docutils literal notranslate"><span class="pre">weights</span></code> is a path to a
model directory, will attempt to read <code class="docutils literal notranslate"><span class="pre">mil_params.json</span></code> from this
location and load saved configuration. Defaults to None.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Outcomes.</p></li>
<li><p><strong>dest</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path at which to save tile predictions.</p></li>
<li><p><strong>uq</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to generate uncertainty estimates. Defaults to False.</p></li>
<li><p><strong>device</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Device on which to run inference. Defaults to None.</p></li>
<li><p><strong>tile_batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Batch size for tile-level predictions. Defaults
to 512.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Attention pooling strategy. Either ‘avg’
or ‘max’. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dataframe of tile predictions.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>pd.DataFrame</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.generate_attention_heatmaps">
<span class="sig-name descname"><span class="pre">generate_attention_heatmaps</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#generate_attention_heatmaps"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.generate_attention_heatmaps" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate and save attention heatmaps for a dataset.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path at which to save heatmap images.</p></li>
<li><p><strong>dataset</strong> (<em>sf.Dataset</em>) – Dataset.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – List of bag file paths.
Each bag should contain PyTorch array of features from all tiles in
a slide, with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><em>np.ndarray</em><em>)</em>) – Attention scores for each slide.
Length of <code class="docutils literal notranslate"><span class="pre">attention</span></code> should equal the length of <code class="docutils literal notranslate"><span class="pre">bags</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>interpolation</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Interpolation strategy for smoothing
heatmap. Defaults to ‘bicubic’.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Matplotlib colormap for heatmap. Can be any
valid matplotlib colormap. Defaults to ‘inferno’.</p></li>
<li><p><strong>norm</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Normalization strategy for assigning heatmap
values to colors. Either ‘two_slope’, or any other valid value
for the <code class="docutils literal notranslate"><span class="pre">norm</span></code> argument of <code class="docutils literal notranslate"><span class="pre">matplotlib.pyplot.imshow</span></code>.
If ‘two_slope’, normalizes values less than 0 and greater than 0
separately. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.generate_mil_features">
<span class="sig-name descname"><span class="pre">generate_mil_features</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">weights</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">sf.Dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><span class="pre">ndarray</span><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil._params.TrainerConfig"><span class="pre">TrainerConfig</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">MILFeatures</span></span></span><a class="reference internal" href="../_modules/slideflow/mil/eval/#generate_mil_features"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.generate_mil_features" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate activations weights from the last layer of an MIL model.</p>
<p>Returns MILFeatures object.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>weights</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path to model weights to load.</p></li>
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Configuration for building model. If <code class="docutils literal notranslate"><span class="pre">weights</span></code> is a path to a
model directory, will attempt to read <code class="docutils literal notranslate"><span class="pre">mil_params.json</span></code> from this
location and load saved configuration. Defaults to None.</p></li>
<li><p><strong>dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Dataset.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Outcomes.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Path to bags, or list of bag file paths.
Each bag should contain PyTorch array of features from all tiles in
a slide, with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

</section>
<section id="trainerconfig">
<h2>TrainerConfig<a class="headerlink" href="#trainerconfig" title="Permalink to this heading">¶</a></h2>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">TrainerConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'attention_mil'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregation_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'slide'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lr</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">wd</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">1e-05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bag_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">512</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_val_bag_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">fit_one_cycle</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">epochs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">32</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">64</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">drop_last</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">save_monitor</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'valid_loss'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">weighted_loss</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/mil/_params/#TrainerConfig"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.TrainerConfig" title="Permalink to this definition">¶</a></dt>
<dd><p>Training configuration for FastAI MIL models.</p>
<p>This configuration should not be created directly, but rather should
be created through <a class="reference internal" href="#slideflow.mil.mil_config" title="slideflow.mil.mil_config"><code class="xref py py-func docutils literal notranslate"><span class="pre">slideflow.mil.mil_config()</span></code></a>, which will create
and prepare an appropriate trainer configuration.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>Callable</em>) – Either the name of a model, or a custom torch
module. Valid model names include <code class="docutils literal notranslate"><span class="pre">&quot;attention_mil&quot;</span></code>,
<code class="docutils literal notranslate"><span class="pre">&quot;transmil&quot;</span></code>, and <code class="docutils literal notranslate"><span class="pre">&quot;bistro.transformer&quot;</span></code>.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>aggregation_level</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – When equal to <code class="docutils literal notranslate"><span class="pre">'slide'</span></code> each bag
contains tiles from a single slide. When equal to <code class="docutils literal notranslate"><span class="pre">'patient'</span></code>
tiles from all slides of a patient are grouped together.</p></li>
<li><p><strong>lr</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a><em>, </em><em>optional</em>) – Learning rate. If <code class="docutils literal notranslate"><span class="pre">fit_one_cycle=True</span></code>,
this is the maximum learning rate. If None, uses the Leslie
Smith <a class="reference external" href="https://arxiv.org/abs/1506.01186">LR Range test</a> to
find an optimal learning rate. Defaults to None.</p></li>
<li><p><strong>wd</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Weight decay. Only used if <code class="docutils literal notranslate"><span class="pre">fit_one_cycle=False</span></code>.
Defaults to 1e-5.</p></li>
<li><p><strong>bag_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Bag size. Defaults to 512.</p></li>
<li><p><strong>max_val_bag_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a><em>, </em><em>optional</em>) – Maximum validation bag size. If
None, all validation bags will be unclipped and unpadded (full size).
Defaults to None.</p></li>
<li><p><strong>fit_one_cycle</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Use <a class="reference external" href="https://sgugger.github.io/the-1cycle-policy.html">1cycle</a>
learning rate schedule. Defaults to True.</p></li>
<li><p><strong>epochs</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Maximum number of epochs. Defaults to 32.</p></li>
<li><p><strong>batch_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Batch size. Defaults to 64.</p></li>
<li><p><strong>**kwargs</strong> – All additional keyword arguments are passed to
<a class="reference internal" href="#slideflow.mil.MILModelConfig" title="slideflow.mil.MILModelConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.MILModelConfig</span></code></a>.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<table class="autosummary longtable docutils align-default">
<tbody>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">TrainerConfig.model_fn</span></code></p></td>
<td><p>MIL model architecture (class/module).</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">TrainerConfig.loss_fn</span></code></p></td>
<td><p>MIL loss function.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">TrainerConfig.is_multimodal</span></code></p></td>
<td><p>Whether the model is multimodal.</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">TrainerConfig.model_type</span></code></p></td>
<td><p>Type of model (classification or regression).</p></td>
</tr>
</tbody>
</table>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.to_dict">
<span class="sig-name descname"><span class="pre">to_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.TrainerConfig.to_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts this training configuration to a dictionary.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.json_dump">
<span class="sig-name descname"><span class="pre">json_dump</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.TrainerConfig.json_dump" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts this training configuration to a JSON-compatible dict.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.is_classification">
<span class="sig-name descname"><span class="pre">is_classification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.TrainerConfig.is_classification" title="Permalink to this definition">¶</a></dt>
<dd><p>Whether the model is a classification model.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.get_metrics">
<span class="sig-name descname"><span class="pre">get_metrics</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.TrainerConfig.get_metrics" title="Permalink to this definition">¶</a></dt>
<dd><p>Get model metrics.</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>List of metrics to use for model evaluation.
Defaults to RocAuc for classification models, and mse and Pearson
correlation coefficient for regression models.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>List[Callable]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.prepare_training">
<span class="sig-name descname"><span class="pre">prepare_training</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_label</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span></span><a class="headerlink" href="#slideflow.mil.TrainerConfig.prepare_training" title="Permalink to this definition">¶</a></dt>
<dd><p>Prepare for training.</p>
<p>Sets up the output directory for the model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Outcomes.</p></li>
<li><p><strong>exp_label</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Experiment label.</p></li>
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Output directory.</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Output directory.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)">str</a></p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.build_model">
<span class="sig-name descname"><span class="pre">build_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_in</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_out</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.TrainerConfig.build_model" title="Permalink to this definition">¶</a></dt>
<dd><p>Build the model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>n_in</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of input features.</p></li>
<li><p><strong>n_out</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of output features.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>**kwargs</strong> – Additional keyword arguments to pass to the model constructor.</p>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>PyTorch model.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>torch.nn.Module</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.predict">
<span class="sig-name descname"><span class="pre">predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</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="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.TrainerConfig.predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate model prediction from bags.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Loaded PyTorch MIL model.</p></li>
<li><p><strong>bags</strong> (<em>torch.Tensor</em>) – Bags, with shape <code class="docutils literal notranslate"><span class="pre">(n_bags,</span> <span class="pre">n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to return attention maps.</p>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Predictions and attention.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray, List[np.ndarray]]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.batched_predict">
<span class="sig-name descname"><span class="pre">batched_predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">loaded_bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Tensor</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.mil.TrainerConfig.batched_predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate predictions from a batch of bags.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Loaded PyTorch MIL model.</p></li>
<li><p><strong>loaded_bags</strong> (<em>torch.Tensor</em>) – Loaded bags, with shape <code class="docutils literal notranslate"><span class="pre">(n_bags,</span> <span class="pre">n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>device</strong> (<em>torch.device</em><em>, </em><em>optional</em>) – Device on which to run the model.
If None, uses the default device.</p></li>
<li><p><strong>forward_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Additional keyword arguments to
pass to the model’s forward function.</p></li>
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to return attention maps.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Attention pooling strategy. Either ‘avg’
or ‘max’. Defaults to ‘avg’.</p></li>
<li><p><strong>uq</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to return uncertainty quantification.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Predictions and attention.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray, List[np.ndarray]]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.train">
<span class="sig-name descname"><span class="pre">train</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">train_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">val_dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mil'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_label</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Learner</span></span></span><a class="headerlink" href="#slideflow.mil.TrainerConfig.train" title="Permalink to this definition">¶</a></dt>
<dd><p>Train a multiple-instance learning (MIL) model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>config</strong> (<a class="reference internal" href="#slideflow.mil.TrainerConfig" title="slideflow.mil.TrainerConfig"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.mil.TrainerConfig</span></code></a>) – Trainer and model configuration.</p></li>
<li><p><strong>train_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Training dataset.</p></li>
<li><p><strong>val_dataset</strong> (<a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.Dataset"><code class="xref py py-class docutils literal notranslate"><span class="pre">slideflow.Dataset</span></code></a>) – Validation dataset.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Outcome column (annotation header) from which to
derive category labels.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Either a path to directory with *.pt files, or a list
of paths to individual *.pt files. Each file should contain
exported feature vectors, with each file containing all tile
features for one patient.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Directory in which to save model and results.</p></li>
<li><p><strong>exp_label</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Experiment label, used for naming the subdirectory
in the <code class="docutils literal notranslate"><span class="pre">{project</span> <span class="pre">root}/mil</span></code> folder, where training history
and the model will be saved.</p></li>
<li><p><strong>attention_heatmaps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Generate attention heatmaps for slides.
Not available for multi-modal MIL models. Defaults to False.</p></li>
<li><p><strong>interpolation</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Interpolation strategy for smoothing
attention heatmaps. Defaults to ‘bicubic’.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Matplotlib colormap for heatmap. Can be any
valid matplotlib colormap. Defaults to ‘inferno’.</p></li>
<li><p><strong>norm</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Normalization strategy for assigning heatmap
values to colors. Either ‘two_slope’, or any other valid value
for the <code class="docutils literal notranslate"><span class="pre">norm</span></code> argument of <code class="docutils literal notranslate"><span class="pre">matplotlib.pyplot.imshow</span></code>.
If ‘two_slope’, normalizes values less than 0 and greater than 0
separately. Defaults to None.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.eval">
<span class="sig-name descname"><span class="pre">eval</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="../dataset/#slideflow.Dataset" title="slideflow.dataset.Dataset"><span class="pre">Dataset</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">outcomes</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="p"><span class="pre">]</span></span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'mil'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention_heatmaps</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uq</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">aggregation_level</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">params</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">heatmap_kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">DataFrame</span></span></span><a class="headerlink" href="#slideflow.mil.TrainerConfig.eval" title="Permalink to this definition">¶</a></dt>
<dd><p>Evaluate a multiple-instance learning model.</p>
<p>Saves results for the evaluation in the target folder, including
predictions (parquet format), attention (Numpy format for each slide),
and attention heatmaps (if <code class="docutils literal notranslate"><span class="pre">attention_heatmaps=True</span></code>).</p>
<p>Logs classifier metrics (AUROC and AP) to the console.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Loaded PyTorch MIL model.</p></li>
<li><p><strong>dataset</strong> (<em>sf.Dataset</em>) – Dataset to evaluation.</p></li>
<li><p><strong>outcomes</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Outcomes.</p></li>
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a><em>(</em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>)</em>) – Path to bags, or list of bag file paths.
Each bag should contain PyTorch array of features from all tiles in
a slide, with the shape <code class="docutils literal notranslate"><span class="pre">(n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Path at which to save results.</p></li>
<li><p><strong>attention_heatmaps</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Generate attention heatmaps for slides.
Not available for multi-modal MIL models. Defaults to False.</p></li>
<li><p><strong>interpolation</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Interpolation strategy for smoothing
attention heatmaps. Defaults to ‘bicubic’.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Matplotlib colormap for heatmap. Can be any
valid matplotlib colormap. Defaults to ‘inferno’.</p></li>
<li><p><strong>norm</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>optional</em>) – Normalization strategy for assigning heatmap
values to colors. Either ‘two_slope’, or any other valid value
for the <code class="docutils literal notranslate"><span class="pre">norm</span></code> argument of <code class="docutils literal notranslate"><span class="pre">matplotlib.pyplot.imshow</span></code>.
If ‘two_slope’, normalizes values less than 0 and greater than 0
separately. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Dataframe of predictions.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>pd.DataFrame</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.build_train_dataloader">
<span class="sig-name descname"><span class="pre">build_train_dataloader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">targets</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">encoder</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset_kwargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataloader_kwargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">torch.utils.DataLoader</span></span></span><a class="headerlink" href="#slideflow.mil.TrainerConfig.build_train_dataloader" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a training dataloader.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a>) – List of bags.</p></li>
<li><p><strong>targets</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a>) – List of targets.</p></li>
<li><p><strong>encoder</strong> (<em>torch.nn.Module</em>) – Encoder for bags.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>dataset_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a>) – Keyword arguments for the dataset.</p></li>
<li><p><strong>dataloader_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a>) – Keyword arguments for the dataloader.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Training dataloader.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>torch.utils.DataLoader</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.build_val_dataloader">
<span class="sig-name descname"><span class="pre">build_val_dataloader</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">targets</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">encoder</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataset_kwargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">dataloader_kwargs</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">torch.utils.DataLoader</span></span></span><a class="headerlink" href="#slideflow.mil.TrainerConfig.build_val_dataloader" title="Permalink to this definition">¶</a></dt>
<dd><p>Build a validation dataloader.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>bags</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a>) – List of bags.</p></li>
<li><p><strong>targets</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.12)"><em>list</em></a>) – List of targets.</p></li>
<li><p><strong>encoder</strong> (<em>torch.nn.Module</em>) – Encoder for bags.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>dataset_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a>) – Keyword arguments for the dataset.</p></li>
<li><p><strong>dataloader_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a>) – Keyword arguments for the dataloader.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Validation dataloader.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>torch.utils.DataLoader</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.inspect_batch">
<span class="sig-name descname"><span class="pre">inspect_batch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.mil.TrainerConfig.inspect_batch" title="Permalink to this definition">¶</a></dt>
<dd><p>Inspect a batch of data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>batch</strong> – One batch of data.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Number of input and output features.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Tuple[<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a>]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.TrainerConfig.run_metrics">
<span class="sig-name descname"><span class="pre">run_metrics</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'slide'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.TrainerConfig.run_metrics" title="Permalink to this definition">¶</a></dt>
<dd><p>Run metrics and save plots to disk.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>df</strong> (<em>pd.DataFrame</em>) – Dataframe with predictions and outcomes.</p></li>
<li><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Level at which to calculate metrics. Either ‘slide’ or ‘patient’.</p></li>
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Output directory for saving metrics.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

</section>
<section id="milmodelconfig">
<h2>MILModelConfig<a class="headerlink" href="#milmodelconfig" title="Permalink to this heading">¶</a></h2>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">MILModelConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'attention_mil'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">use_lens</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apply_softmax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">loss</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Callable" title="(in Python v3.12)"><span class="pre">Callable</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'cross_entropy'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow/mil/_params/#MILModelConfig"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.mil.MILModelConfig" title="Permalink to this definition">¶</a></dt>
<dd><p>Model configuration for an MIL model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>Callable</em>) – Either the name of a model, or a custom torch
module. Valid model names include <code class="docutils literal notranslate"><span class="pre">&quot;attention_mil&quot;</span></code> and
<code class="docutils literal notranslate"><span class="pre">&quot;transmil&quot;</span></code>. Defaults to ‘attention_mil’.</p>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>use_lens</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a><em>, </em><em>optional</em>) – Whether the model expects a second
argument to its <code class="docutils literal notranslate"><span class="pre">.forward()</span></code> function, an array with the
bag size for each slide. If None, will default to True for
<code class="docutils literal notranslate"><span class="pre">'attention_mil'</span></code> models and False otherwise.
Defaults to None.</p></li>
<li><p><strong>apply_softmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to apply softmax to model outputs.
Defaults to True. Ignored if the model is not a classification
model.</p></li>
<li><p><strong>model_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Additional keyword arguments to pass
to the model constructor. Defaults to None.</p></li>
<li><p><strong>validate</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to validate the keyword arguments. If True,
will raise an error if any unrecognized keyword arguments are
passed. Defaults to True.</p></li>
<li><p><strong>loss</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a><em>, </em><em>Callable</em>) – Loss function. Defaults to ‘cross_entropy’.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<table class="autosummary longtable docutils align-default">
<tbody>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">MILModelConfig.apply_softmax</span></code></p></td>
<td><p>Whether softmax will be applied to model outputs.</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">MILModelConfig.loss_fn</span></code></p></td>
<td><p>MIL loss function.</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">MILModelConfig.model_fn</span></code></p></td>
<td><p>MIL model architecture (class/module).</p></td>
</tr>
<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">MILModelConfig.model_type</span></code></p></td>
<td><p>Type of model (classification or regression).</p></td>
</tr>
<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">MILModelConfig.is_multimodal</span></code></p></td>
<td><p>Whether the model is multimodal.</p></td>
</tr>
</tbody>
</table>
<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig.is_classification">
<span class="sig-name descname"><span class="pre">is_classification</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.MILModelConfig.is_classification" title="Permalink to this definition">¶</a></dt>
<dd><p>Whether the model is a classification model.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig.to_dict">
<span class="sig-name descname"><span class="pre">to_dict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.MILModelConfig.to_dict" title="Permalink to this definition">¶</a></dt>
<dd><p>Converts this model configuration to a dictionary.</p>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig.inspect_batch">
<span class="sig-name descname"><span class="pre">inspect_batch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">batch</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.mil.MILModelConfig.inspect_batch" title="Permalink to this definition">¶</a></dt>
<dd><p>Inspect a batch of data.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><p><strong>batch</strong> – One batch of data.</p>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p>Number of input and output features.</p>
</dd>
<dt class="field-odd">Return type<span class="colon">:</span></dt>
<dd class="field-odd"><p>Tuple[<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a>, <a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)">int</a>]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig.build_model">
<span class="sig-name descname"><span class="pre">build_model</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_in</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_out</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.MILModelConfig.build_model" title="Permalink to this definition">¶</a></dt>
<dd><p>Build the model.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>n_in</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of input features.</p></li>
<li><p><strong>n_out</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of output features.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><p><strong>**kwargs</strong> – Additional keyword arguments to pass to the model constructor.</p>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>PyTorch model.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>torch.nn.Module</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig.predict">
<span class="sig-name descname"><span class="pre">predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bags</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</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">apply_softmax</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#slideflow.mil.MILModelConfig.predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate model prediction from bags.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Loaded PyTorch MIL model.</p></li>
<li><p><strong>bags</strong> (<em>torch.Tensor</em>) – Bags, with shape <code class="docutils literal notranslate"><span class="pre">(n_bags,</span> <span class="pre">n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to return attention maps.</p></li>
<li><p><strong>apply_softmax</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to apply softmax to model outputs.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to pool attention maps with
average pooling. Defaults to None.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Predictions and attention.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray, List[np.ndarray]]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig.batched_predict">
<span class="sig-name descname"><span class="pre">batched_predict</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Module</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">loaded_bags</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Tensor</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Any" title="(in Python v3.12)"><span class="pre">Any</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">forward_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">attention_pooling</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">uq</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apply_softmax</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.Tuple" title="(in Python v3.12)"><span class="pre">Tuple</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/typing.html#typing.List" title="(in Python v3.12)"><span class="pre">List</span></a><span class="p"><span class="pre">[</span></span><span class="pre">ndarray</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#slideflow.mil.MILModelConfig.batched_predict" title="Permalink to this definition">¶</a></dt>
<dd><p>Generate predictions from a batch of bags.</p>
<p>More efficient than calling <a class="reference internal" href="#slideflow.mil.MILModelConfig.predict" title="slideflow.mil.MILModelConfig.predict"><code class="xref py py-meth docutils literal notranslate"><span class="pre">predict()</span></code></a> multiple times.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<em>torch.nn.Module</em>) – Loaded PyTorch MIL model.</p></li>
<li><p><strong>loaded_bags</strong> (<em>torch.Tensor</em>) – Loaded bags, with shape <code class="docutils literal notranslate"><span class="pre">(n_bags,</span> <span class="pre">n_tiles,</span> <span class="pre">n_features)</span></code>.</p></li>
</ul>
</dd>
<dt class="field-even">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>device</strong> (<em>torch.device</em><em>, </em><em>optional</em>) – Device on which to run the model.
If None, uses the default device.</p></li>
<li><p><strong>forward_kwargs</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><em>dict</em></a><em>, </em><em>optional</em>) – Additional keyword arguments to
pass to the model’s forward function.</p></li>
<li><p><strong>attention</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to return attention maps.</p></li>
<li><p><strong>attention_pooling</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Attention pooling strategy. Either ‘avg’
or ‘max’. Defaults to None.</p></li>
<li><p><strong>uq</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Whether to return uncertainty quantification.</p></li>
</ul>
</dd>
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p>Predictions and attention.</p>
</dd>
<dt class="field-even">Return type<span class="colon">:</span></dt>
<dd class="field-even"><p>Tuple[np.ndarray, List[np.ndarray]]</p>
</dd>
</dl>
</dd></dl>

<dl class="py function">
<dt class="sig sig-object py" id="slideflow.mil.MILModelConfig.run_metrics">
<span class="sig-name descname"><span class="pre">run_metrics</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">self</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">df</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'slide'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">outdir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span></span><a class="headerlink" href="#slideflow.mil.MILModelConfig.run_metrics" title="Permalink to this definition">¶</a></dt>
<dd><p>Run metrics and save plots to disk.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>df</strong> (<em>pd.DataFrame</em>) – Dataframe with predictions and outcomes.</p></li>
<li><p><strong>level</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Level at which to calculate metrics. Either ‘slide’ or ‘patient’.</p></li>
<li><p><strong>outdir</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Output directory for saving metrics.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

</section>
<section id="clammodelconfig">
<h2>CLAMModelConfig<a class="headerlink" href="#clammodelconfig" title="Permalink to this heading">¶</a></h2>
<p>The CLAM model configuration class requires <code class="docutils literal notranslate"><span class="pre">slideflow-gpl</span></code>, which can be installed with:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>slideflow-gpl
</pre></div>
</div>
<p>Once installed, the class is available at <code class="docutils literal notranslate"><span class="pre">slideflow.clam.CLAMModelConfig</span></code>.</p>
<dl class="py class">
<dt class="sig sig-object py" id="slideflow.clam.CLAMModelConfig">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-name descname"><span class="pre">CLAMModelConfig</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'clam_sb'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">*</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_size</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'small'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bag_loss</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'ce'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">bag_weight</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><span class="pre">float</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">0.7</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="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">opt</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'adam'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inst_loss</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><span class="pre">str</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">'ce'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_inst_cluster</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">B</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><span class="pre">int</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">8</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">model_kwargs</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.12)"><span class="pre">dict</span></a><span class="w"> </span><span class="p"><span class="pre">|</span></span><span class="w"> </span><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.12)"><span class="pre">None</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">validate</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><span class="pre">bool</span></a></span><span class="w"> </span><span class="o"><span class="pre">=</span></span><span class="w"> </span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/slideflow_gpl/clam/config/#CLAMModelConfig"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#slideflow.clam.CLAMModelConfig" title="Permalink to this definition">¶</a></dt>
<dd><p>Model configuration for CLAM models.</p>
<p>These configuration options are identical to the options in the
<a class="reference external" href="https://arxiv.org/abs/2004.09666">original CLAM paper</a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Keyword Arguments<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Model. Either <code class="docutils literal notranslate"><span class="pre">'clam_sb'</span></code>, <code class="docutils literal notranslate"><span class="pre">'clam_mb'</span></code>,
<code class="docutils literal notranslate"><span class="pre">'mil_fc'</span></code>, or <code class="docutils literal notranslate"><span class="pre">'mil_fc_mc'</span></code>. Defaults to <code class="docutils literal notranslate"><span class="pre">'clam_sb'</span></code>.</p></li>
<li><p><strong>model_size</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – <p>Size of the model. Available sizes include:</p>
<p><code class="docutils literal notranslate"><span class="pre">clam_sb</span></code></p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>small</p></td>
<td><p>[1024, 512, 256]</p></td>
</tr>
<tr class="row-even"><td><p>big</p></td>
<td><p>[1024, 512, 384]</p></td>
</tr>
<tr class="row-odd"><td><p>multiscale</p></td>
<td><p>[2048, 512, 256]</p></td>
</tr>
<tr class="row-even"><td><p>xception</p></td>
<td><p>[2048, 256, 128]</p></td>
</tr>
<tr class="row-odd"><td><p>xception_multi</p></td>
<td><p>[1880, 128, 64]</p></td>
</tr>
<tr class="row-even"><td><p>xception_3800</p></td>
<td><p>[3800, 512, 256]</p></td>
</tr>
</tbody>
</table>
<p><code class="docutils literal notranslate"><span class="pre">clam_mb</span></code></p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>small</p></td>
<td><p>[1024, 512, 256]</p></td>
</tr>
<tr class="row-even"><td><p>big</p></td>
<td><p>[1024, 512, 384]</p></td>
</tr>
<tr class="row-odd"><td><p>multiscale</p></td>
<td><p>[2048, 512, 256]</p></td>
</tr>
</tbody>
</table>
<p><code class="docutils literal notranslate"><span class="pre">mil_fc</span></code></p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>small</p></td>
<td><p>[1024, 512]</p></td>
</tr>
</tbody>
</table>
<p><code class="docutils literal notranslate"><span class="pre">mil_fc_mc</span></code></p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>small</p></td>
<td><p>[1024, 512]</p></td>
</tr>
</tbody>
</table>
</p></li>
<li><p><strong>bag_loss</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Primary loss function. Either ‘ce’ or ‘svm’.
If ‘ce’, the model loss function is a cross entropy loss.
If ‘svm’, the model loss is topk.SmoothTop1SVM.
Defaults to ‘ce’.</p></li>
<li><p><strong>bag_weight</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.12)"><em>float</em></a>) – Weight of the bag loss. The total loss is
defined0 as <code class="docutils literal notranslate"><span class="pre">W</span> <span class="pre">*</span> <span class="pre">loss</span> <span class="pre">+</span> <span class="pre">(1</span> <span class="pre">-</span> <span class="pre">W)</span> <span class="pre">*</span> <span class="pre">instance_loss</span></code>, where
<code class="docutils literal notranslate"><span class="pre">W</span></code> is the bag weight. Defaults to 0.7</p></li>
<li><p><strong>dropout</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Add dropout (p=0.25) after the attention layers.
Defaults to False.</p></li>
<li><p><strong>opt</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Optimizer. Either ‘adam’ (Adam optimizer) or ‘sgd’
(Stochastic Gradient Descent). Defaults to ‘adam’.</p></li>
<li><p><strong>inst_loss</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.12)"><em>str</em></a>) – Instance loss function. Either ‘ce’ or ‘svm’.
If ‘ce’, the instance loss is a cross entropy loss.
If ‘svm’, the loss is topk.SmoothTop1SVM.
Defaults to ‘ce’.</p></li>
<li><p><strong>no_inst_cluster</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Disable instance-level clustering.
Defaults to False.</p></li>
<li><p><strong>B</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.12)"><em>int</em></a>) – Number of positive/negative patches to sample for
instance-level training. Defaults to 8.</p></li>
<li><p><strong>validate</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.12)"><em>bool</em></a>) – Validate the hyperparameter configuration.
Defaults to True.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

</section>
</section>


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