Developer

Benchmarking

.. module:: nichecompass.benchmarking
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    benchmarking.utils.compute_knn_graph_connectivities_and_distances

Data

.. 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

.. module:: nichecompass.models
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    models.utils.load_saved_files
    models.utils.validate_var_names
    models.utils.initialize_model

Modules

.. 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

.. 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

.. module:: nichecompass.train
.. currentmodule:: nichecompass

.. autosummary::
    :toctree: generated

    train.Trainer
    train.eval_metrics
    train.plot_eval_metrics