.gitignore
LICENSE
README.md
pyproject.toml
setup.py
adjacency_matrices_plots/adjacency_matrices_plots.ipynb
attention_visualisation/attn_graph_darmanis_igraph.ipynb
attention_visualisation/attn_graph_pbmc_igraph.ipynb
attention_visualisation/attn_heatmap_darmanis_mean_heads.ipynb
attention_visualisation/attn_heatmap_darmanis_per_head.ipynb
attention_visualisation/attn_heatmap_pbmc_all_mean_heads.ipynb
attention_visualisation/attn_heatmap_pbmc_per_head.ipynb
attention_visualisation/darmanis_layer_2_graph_ORIGINAL.pdf
attention_visualisation/latent_space_euclidean_distance.ipynb
attention_visualisation/pbmc_layer_2_graph_ORIGINAL.pdf
attention_visualisation/Darmanis/darmanis_ground_truth_clusters.csv
attention_visualisation/Darmanis/CellVGAE/cellvgae_clusters.npy
attention_visualisation/Darmanis/CellVGAE/cellvgae_node_embs.npy
attention_visualisation/Darmanis/CellVGAE/cellvgae_umap.npy
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_1_attention_coeff.pt
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_1_attention_edge_index.pt
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_2_attention_coeff.pt
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_2_attention_edge_index.pt
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_mean_attention_coeff.pt
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_mean_attention_edge_index.pt
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_std_attention_coeff.pt
attention_visualisation/Darmanis/attn_layers_data/darmanis_hidden_layer_std_attention_edge_index.pt
attention_visualisation/PBMC3k/seurat_clusters.csv
attention_visualisation/PBMC3k/CellVGAE/cellvgae_clusters.npy
attention_visualisation/PBMC3k/CellVGAE/cellvgae_node_embs.npy
attention_visualisation/PBMC3k/CellVGAE/cellvgae_umap.npy
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_1_attention_coeff.pt
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_1_attention_edge_index.pt
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_2_attention_coeff.pt
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_2_attention_edge_index.pt
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_mean_attention_coeff.pt
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_mean_attention_edge_index.pt
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_std_attention_coeff.pt
attention_visualisation/PBMC3k/attn_layers_data/pbmc3k_hidden_layer_std_attention_edge_index.pt
attention_visualisation/PDFs/darmanis_umap_layer2_mean.pdf
attention_visualisation/PDFs/pbmc3k_umap_layer2_mean.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_1st.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_1st_DIFF.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_2nd.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_2nd_DIFF.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_mu.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_mu_DIFF.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_sigma.pdf
attention_visualisation/PDFs/attention_heads/darmanis_umap_layer_sigma_DIFF.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_1st.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_1st_DIFF.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_2nd.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_2nd_DIFF.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_mu.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_mu_DIFF.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_std.pdf
attention_visualisation/PDFs/attention_heads/pbmc3k_umap_layer_std_DIFF.pdf
cellvgae/__init__.py
cellvgae/__main__.py
cellvgae.egg-info/PKG-INFO
cellvgae.egg-info/SOURCES.txt
cellvgae.egg-info/dependency_links.txt
cellvgae.egg-info/requires.txt
cellvgae.egg-info/top_level.txt
cellvgae/models/CellVGAE.py
cellvgae/models/CellVGAE_Encoder.py
cellvgae/models/__init__.py
cellvgae/models/mmd.py
cellvgae/utils/__init__.py
cellvgae/utils/attn_graph.py
cellvgae/utils/top_genes.py
example_data/paul15_Faiss_KNN_K3_KHVG2500.txt
example_data/paul15_myeloid_scanpy.h5ad
examples/cellvgae_example_scripts.txt
figures/workflow.png
misc/benchmark_sam.ipynb
misc/clean_seger.ipynb
misc/clean_wang.ipynb
misc/curate_baron.ipynb
platelet_knn_analysis/PBMC3k_HVG_250_KNN_k20.txt
platelet_knn_analysis/PBMC3k_HVG_seurat_250.csv
platelet_knn_analysis/platelet_knn_analysis.ipynb
platelet_knn_analysis/seurat_clusters.csv
preprocessing/generate_knn.ipynb
preprocessing/hvg_proprocessing.ipynb
saved_embeddings/inspect_saved.ipynb
saved_embeddings/baron1/Baron1_ground_truth.csv
saved_embeddings/baron1/clusters.npy
saved_embeddings/baron1/labels_comparison.csv
saved_embeddings/baron1/metadata.csv
saved_embeddings/baron1/node_embs.npy
saved_embeddings/baron1/umap.npy
saved_embeddings/baron2/Baron2_ground_truth.csv
saved_embeddings/baron2/clusters.npy
saved_embeddings/baron2/labels_comparison.csv
saved_embeddings/baron2/metadata.csv
saved_embeddings/baron2/node_embs.npy
saved_embeddings/baron2/umap.npy
saved_embeddings/baron3/Baron3_ground_truth.csv
saved_embeddings/baron3/clusters.npy
saved_embeddings/baron3/labels_comparison.csv
saved_embeddings/baron3/metadata.csv
saved_embeddings/baron3/node_embs.npy
saved_embeddings/baron3/umap.npy
saved_embeddings/baron4/Baron4_ground_truth.csv
saved_embeddings/baron4/clusters.npy
saved_embeddings/baron4/labels_comparison.csv
saved_embeddings/baron4/metadata.csv
saved_embeddings/baron4/node_embs.npy
saved_embeddings/baron4/umap.npy
saved_embeddings/darmanis/clusters.npy
saved_embeddings/darmanis/darmanis_ground_truth.csv
saved_embeddings/darmanis/labels_comparison.csv
saved_embeddings/darmanis/metadata.csv
saved_embeddings/darmanis/node_embs.npy
saved_embeddings/darmanis/umap.npy
saved_embeddings/loh/clusters.npy
saved_embeddings/loh/labels_comparison.csv
saved_embeddings/loh/loh_ground_truth.csv
saved_embeddings/loh/metadata.csv
saved_embeddings/loh/node_embs.npy
saved_embeddings/loh/umap.npy
saved_embeddings/muraro/clusters.npy
saved_embeddings/muraro/labels_comparison.csv
saved_embeddings/muraro/metadata.csv
saved_embeddings/muraro/muraro_ground_truth.csv
saved_embeddings/muraro/node_embs.npy
saved_embeddings/muraro/umap.npy
saved_embeddings/plots_with_sam_embeddings/all_datasets_plots.ipynb
saved_embeddings/plots_with_sam_embeddings/sam_umaps.npy
saved_embeddings/segerstolpe/clusters.npy
saved_embeddings/segerstolpe/labels_comparison.csv
saved_embeddings/segerstolpe/metadata.csv
saved_embeddings/segerstolpe/node_embs.npy
saved_embeddings/segerstolpe/seger_ground_truth.csv
saved_embeddings/segerstolpe/umap.npy
saved_embeddings/wang/clusters.npy
saved_embeddings/wang/labels_comparison.csv
saved_embeddings/wang/metadata.csv
saved_embeddings/wang/node_embs.npy
saved_embeddings/wang/umap.npy
saved_embeddings/wang/wang_ground_truth.csv
top_genes/top_genes.ipynb
top_genes/schisto_example/CellVGAE/cellvgae_clusters.npy
top_genes/schisto_example/CellVGAE/cellvgae_node_embs.npy
top_genes/schisto_example/CellVGAE/cellvgae_umap.npy
top_genes/schisto_example/HVG/Schisto_HVG_250.csv
top_genes/schisto_example/layer_weights/schisto_hidden_layer_1_weight.pt
top_genes/schisto_example/layer_weights/schisto_hidden_layer_2_weight.pt
top_genes/schisto_example/layer_weights/schisto_hidden_layer_mean_weight.pt
top_genes/schisto_example/layer_weights/schisto_hidden_layer_std_weight.pt