--- a
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+.. _mil_api:
+
+.. currentmodule:: slideflow.mil
+
+slideflow.mil
+==============
+
+This submodule contains tools for multiple-instance learning (MIL) model training and evaluation. See :ref:`mil` for more information. A summary of the API is given below.
+
+**Training:**
+    - :func:`train_mil()`: Train an MIL model, using an MIL configuration, Datasets, and a directory of bags.
+    - :func:`build_fastai_learner()`: Build and return the FastAI Learner, but do not execute training. Useful for customizing training.
+    - :func:`build_multimodal_learner()`: Build and return a FastAI Learner designed for multi-modal/multi-magnification input.
+
+**Evaluation/Inference:**
+    - :func:`eval_mil()`: Evaluate an MIL model using a path to a saved model, a Dataset, and path to bags. Generates metrics.
+    - :func:`predict_mil()`: Generate predictions from an MIL model and saved bags. Returns a pandas dataframe.
+    - :func:`predict_multimodal_mil()`: Generate predictions from a multimodal MIL model. Returns a dataframe.
+    - :func:`predict_slide()`: Generate MIL predictions for a single slide. Returns a 2D array of predictions and attention.
+    - :func:`predict_from_bags()`: Low-level interface for generating predictions from a loaded MIL model and pre-loaded bag Tensors.
+    - :func:`predict_from_multimodal_bags()`: Low-level interface for generating multimodal predictions from a loaded MIL model and bag Tensors.
+    - :func:`get_mil_tile_predictions()`: Get tile-level predictions and attention from a saved MIL model for a given Dataset and saved bags.
+    - :func:`generate_attention_heatmaps()`: Generate and save attention heatmaps.
+    - :func:`generate_mil_features()`: Get last-layer activations from an MIL model. Returns an MILFeatures object.
+
+
+Main functions
+**************
+
+.. autofunction:: mil_config
+.. autofunction:: train_mil
+.. autofunction:: build_fastai_learner
+.. autofunction:: build_multimodal_learner
+.. autofunction:: eval_mil
+.. autofunction:: predict_mil
+.. autofunction:: predict_multimodal_mil
+.. autofunction:: predict_from_bags
+.. autofunction:: predict_from_multimodal_bags
+.. autofunction:: predict_slide
+.. autofunction:: get_mil_tile_predictions
+.. autofunction:: generate_attention_heatmaps
+.. autofunction:: generate_mil_features
+
+TrainerConfig
+*************
+
+.. autoclass:: slideflow.mil.TrainerConfig
+.. autosummary::
+
+    TrainerConfig.model_fn
+    TrainerConfig.loss_fn
+    TrainerConfig.is_multimodal
+    TrainerConfig.model_type
+
+.. autofunction:: slideflow.mil.TrainerConfig.to_dict
+.. autofunction:: slideflow.mil.TrainerConfig.json_dump
+.. autofunction:: slideflow.mil.TrainerConfig.is_classification
+.. autofunction:: slideflow.mil.TrainerConfig.get_metrics
+.. autofunction:: slideflow.mil.TrainerConfig.prepare_training
+.. autofunction:: slideflow.mil.TrainerConfig.build_model
+.. autofunction:: slideflow.mil.TrainerConfig.predict
+.. autofunction:: slideflow.mil.TrainerConfig.batched_predict
+.. autofunction:: slideflow.mil.TrainerConfig.train
+.. autofunction:: slideflow.mil.TrainerConfig.eval
+.. autofunction:: slideflow.mil.TrainerConfig.build_train_dataloader
+.. autofunction:: slideflow.mil.TrainerConfig.build_val_dataloader
+.. autofunction:: slideflow.mil.TrainerConfig.inspect_batch
+.. autofunction:: slideflow.mil.TrainerConfig.run_metrics
+
+MILModelConfig
+**************
+
+.. autoclass:: MILModelConfig
+.. autosummary::
+
+    MILModelConfig.apply_softmax
+    MILModelConfig.loss_fn
+    MILModelConfig.model_fn
+    MILModelConfig.model_type
+    MILModelConfig.is_multimodal
+
+.. autofunction:: slideflow.mil.MILModelConfig.is_classification
+.. autofunction:: slideflow.mil.MILModelConfig.to_dict
+.. autofunction:: slideflow.mil.MILModelConfig.inspect_batch
+.. autofunction:: slideflow.mil.MILModelConfig.build_model
+.. autofunction:: slideflow.mil.MILModelConfig.predict
+.. autofunction:: slideflow.mil.MILModelConfig.batched_predict
+.. autofunction:: slideflow.mil.MILModelConfig.run_metrics
+
+CLAMModelConfig
+***************
+
+The CLAM model configuration class requires ``slideflow-gpl``, which can be installed with:
+
+.. code-block:: bash
+
+    pip install slideflow-gpl
+
+Once installed, the class is available at ``slideflow.clam.CLAMModelConfig``.
+
+.. autoclass:: slideflow.clam.CLAMModelConfig
+