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+++ b/docs/api/developer.md
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+# 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
+```