# Developer

## Benchmarking

```{eval-rst}

.. module:: nichecompass.benchmarking

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    benchmarking.utils.compute_knn_graph_connectivities_and_distances

```

## Data

```{eval-rst}

.. module:: nichecompass.data

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    data.initialize_dataloaders

    data.edge_level_split

    data.node_level_split_mask

    data.prepare_data

    data.SpatialAnnTorchDataset

```

## Models

```{eval-rst}

.. module:: nichecompass.models

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    models.utils.load_saved_files

    models.utils.validate_var_names

    models.utils.initialize_model

```

## Modules

```{eval-rst}

.. module:: nichecompass.modules

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    modules.VGPGAE

    modules.VGAEModuleMixin

    modules.BaseModuleMixin

    modules.compute_cat_covariates_contrastive_loss

    modules.compute_edge_recon_loss

    modules.compute_gp_group_lasso_reg_loss

    modules.compute_gp_l1_reg_loss

    modules.compute_kl_reg_loss

    modules.compute_omics_recon_nb_loss

```

## NN

```{eval-rst}

.. module:: nichecompass.nn

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    nn.OneHopAttentionNodeLabelAggregator

    nn.OneHopGCNNormNodeLabelAggregator

    nn.OneHopSumNodeLabelAggregator

    nn.CosineSimGraphDecoder

    nn.FCOmicsFeatureDecoder

    nn.MaskedOmicsFeatureDecoder

    nn.Encoder

    nn.MaskedLinear

    nn.AddOnMaskedLayer

```

## Train

```{eval-rst}

.. module:: nichecompass.train

.. currentmodule:: nichecompass

.. autosummary::

    :toctree: generated

    train.Trainer

    train.eval_metrics

    train.plot_eval_metrics

```