GHIST+ bundle clean public release

.gitattributes

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+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.avro filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.lz4 filter=lfs diff=lfs merge=lfs -text
+*.mds filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text
+# Audio files - uncompressed
+*.pcm filter=lfs diff=lfs merge=lfs -text
+*.sam filter=lfs diff=lfs merge=lfs -text
+*.raw filter=lfs diff=lfs merge=lfs -text
+# Audio files - compressed
+*.aac filter=lfs diff=lfs merge=lfs -text
+*.flac filter=lfs diff=lfs merge=lfs -text
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+# Image files - uncompressed
+*.bmp filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.tiff filter=lfs diff=lfs merge=lfs -text
+# Image files - compressed
+*.jpg filter=lfs diff=lfs merge=lfs -text
+*.jpeg filter=lfs diff=lfs merge=lfs -text
+*.webp filter=lfs diff=lfs merge=lfs -text
+# Video files - compressed
+*.mp4 filter=lfs diff=lfs merge=lfs -text
+*.webm filter=lfs diff=lfs merge=lfs -text
+other_models/across_slide/GHIST_pred_expr.csv filter=lfs diff=lfs merge=lfs -text
+other_models/imputation/pasta/slide_1_pasta_holdout_pred.csv filter=lfs diff=lfs merge=lfs -text
+other_models/across_slide/SpatialEx_pred_expr.csv filter=lfs diff=lfs merge=lfs -text
+other_models/within_slide/GHIST_pred_expr.csv filter=lfs diff=lfs merge=lfs -text
+other_models/across_slide/Phoenix_pred_expr.csv filter=lfs diff=lfs merge=lfs -text
+other_models/within_slide/SpatialEx_pred_expr.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/breast_multi/test_slide3_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/breast_multi/breast5k/test_slide6_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/breast_multi/breast5k/test_slide6_pred_celltype_probs.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/breast_multi/breast5k/test_slide6_pred_celltype.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/breast_multi/atera/test_slide9101_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/breast_multi/atera/test_slide9101_pred_celltype_probs.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/pancreas3/test_slide14_pred_expr_counts.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/pancreas3/test_slide14_pred_celltype_probs.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/pancreas3/test_slide14_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/breast_5k/test_slide11_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/breast_5k/test_slide11_pred_celltype.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/breast_5k/test_slide11_pred_celltype_probs.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/breast_5k/test_slide11_pred_expr_counts.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/lung_5k/test_slide16_pred_celltype_probs.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/lung_5k/test_slide16_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/pancancer/lung_5k/test_slide16_pred_expr_counts.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/breast_single/trainval_slide3_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/vq_off/vq_composition_off_trainval_slide3_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/vq_off/randomized_vq_composition_trainval_slide3_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+GHIST_plus/predictions/vq_off/trainval_slide3_pred_expr_scaled.csv filter=lfs diff=lfs merge=lfs -text
+evaluation_data/breast5k/cell_coords_histology_filtered.csv filter=lfs diff=lfs merge=lfs -text
+evaluation_data/breast5k/cell_gene_matrix_filtered.csv filter=lfs diff=lfs merge=lfs -text
+evaluation_data/atera/cell_gene_matrix_filtered.csv filter=lfs diff=lfs merge=lfs -text
+evaluation_data/breast2/cell_gene_matrix_filtered.csv filter=lfs diff=lfs merge=lfs -text

GHIST_plus/models/breast_multi/config_inference_atera_domain0.json

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+{
+  "comps": {
+    "avgexp": true,
+    "celltype": true,
+    "crossattn": true,
+    "use_neighb": true,
+    "neighb": true
+  },
+  "regions_val": {
+    "divisions": [
+      [
+        0.0,
+        0.2
+      ]
+    ]
+  },
+  "regions_test": {
+    "divisions": [
+      [
+        0.0,
+        1.0
+      ]
+    ]
+  },
+  "data": {
+    "cell_types": [
+      "B",
+      "Myeloid (excluding macrophage)",
+      "Stromal",
+      "Macrophage",
+      "Malignant",
+      "Epithelial",
+      "Plasma",
+      "T",
+      "Unassigned"
+    ],
+    "min_nuc_area": 10,
+    "expr_scale": 2.0,
+    "foundation_model_input_normalization": "uni2_imagenet",
+    "num_workers": 32,
+    "hsize": 224,
+    "wsize": 224,
+    "overlap": 30,
+    "max_cells_per_patch": 2048,
+    "pin_memory": false
+  },
+  "model": {
+    "foundation_model": {
+      "enabled": true,
+      "pretrained": true,
+      "train_adapter": false
+    },
+    "emb_dim": 1024,
+    "avgexp_temp": 1.0,
+    "avgexp_residual_scale": 1.0,
+    "refiner_query_tokens": 8,
+    "hurdle": {
+      "enabled": true,
+      "sigma_init": 0.5,
+      "sigma_floor": 0.03
+    },
+    "ecrm": {
+      "k_target": 12,
+      "k_min": 6,
+      "k_max": 16,
+      "graph_k": 12,
+      "cross_patch_k": 8,
+      "density_gamma": 0.4,
+      "eta_max": 0.6,
+      "gamma_perp_max": 0.3,
+      "trust_floor": 0.35,
+      "trust_scale": 0.65,
+      "depth": 1,
+      "cross_patch": true,
+      "edge_dropout": 0.0,
+      "message_dropout": 0.0,
+      "residual_gate_init": -1.0,
+      "cross_patch_radius": 512.0,
+      "ct_same_type_only": true,
+      "ct_conf_min": 0.2,
+      "apply_to_embeddings": false,
+      "apply_to_ref_weights": false,
+      "apply_to_expr_residual": true,
+      "use_gt_ct": false,
+      "enabled": true,
+      "ablation_off": false
+    },
+    "vq_patch": {
+      "enabled": true,
+      "n_codes": 64,
+      "beta": 0.25,
+      "use_cosine": true,
+      "inject_cell": false,
+      "loss_w": 0.05
+    },
+    "ct_priors_ecrm_unit_enabled": true
+  },
+  "training": {
+    "batch_size": 64,
+    "total_epochs": 30,
+    "learning_rate": 0.00115,
+    "beta1": 0.9,
+    "beta2": 0.999,
+    "weight_decay": 0.00001,
+    "eps": 1E-8,
+    "stain_aug": true,
+    "uniform_sampler": true,
+    "immune_sampler_boost": 1.0,
+    "panel_completion_loss_weight": 0.0,
+    "panel_hide_frac": 0.0,
+    "panel_use_natural_missing": false,
+    "pearson_loss_weight": 0.0,
+    "expr_var_penalty_weight": 0.0,
+    "use_expr_baseline": false,
+    "holdout_n_genes": 0,
+    "batch_sampler_seed": 20260419,
+    "seed": 20260807
+  },
+  "evaluation": {
+    "parity_tolerance_abs": 0.001,
+    "external_source": "data_sources_test",
+    "external_every_epochs": 1,
+    "external_final_epoch": true
+  },
+  "save_freqs": {
+    "model_freq": 1
+  },
+  "experiment_dirs": {
+    "load_dir": "results",
+    "metrics_dir": "metrics",
+    "model_dir": "models"
+  },
+  "stain_norm": {
+    "norm_train": true,
+    "norm_val": true,
+    "norm_test": true,
+    "fp_norm_ref": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+    "resized_scale": 0.2
+  },
+  "data_sources_train_val": [
+    {
+      "slide_idx": 0,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 1,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast3/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 5,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast4/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 2,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast5/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 4,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast7/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/matched_nuclei_filtered.csv"
+    }
+  ],
+  "data_sources_test": [
+    {
+      "slide_idx": 9101,
+      "domain_id": 0,
+      "fp_nuc_seg": "${ATERA_DATA_ROOT}/ghist_plus/data_processing/he_image_nuclei_seg.tif",
+      "fp_hist": "${ATERA_DATA_ROOT}/WTA_Preview_FFPE_Breast_Cancer_he_image.ome.tif",
+      "fp_expr": "",
+      "fp_cell_type": "",
+      "fp_nuc_sizes": "${ATERA_DATA_ROOT}/ghist_plus/data_processing/matched_nuclei_filtered.csv",
+      "cell_coords_id_space": "histology"
+    }
+  ]
+}

GHIST_plus/models/breast_multi/config_inference_breast5k_domain0.json

@@ -0,0 +1,198 @@
+{
+  "comps": {
+    "avgexp": true,
+    "celltype": true,
+    "crossattn": true,
+    "use_neighb": true,
+    "neighb": true
+  },
+  "regions_val": {
+    "divisions": [
+      [
+        0.0,
+        0.2
+      ]
+    ]
+  },
+  "regions_test": {
+    "divisions": [
+      [
+        0.0,
+        1.0
+      ]
+    ]
+  },
+  "data": {
+    "cell_types": [
+      "B",
+      "Myeloid (excluding macrophage)",
+      "Stromal",
+      "Macrophage",
+      "Malignant",
+      "Epithelial",
+      "Plasma",
+      "T",
+      "Unassigned"
+    ],
+    "min_nuc_area": 10,
+    "expr_scale": 2.0,
+    "foundation_model_input_normalization": "uni2_imagenet",
+    "num_workers": 32,
+    "hsize": 224,
+    "wsize": 224,
+    "overlap": 30,
+    "max_cells_per_patch": 2048,
+    "pin_memory": false
+  },
+  "model": {
+    "foundation_model": {
+      "enabled": true,
+      "pretrained": true,
+      "train_adapter": false
+    },
+    "emb_dim": 1024,
+    "avgexp_temp": 1.0,
+    "avgexp_residual_scale": 1.0,
+    "refiner_query_tokens": 8,
+    "hurdle": {
+      "enabled": true,
+      "sigma_init": 0.5,
+      "sigma_floor": 0.03
+    },
+    "ecrm": {
+      "k_target": 12,
+      "k_min": 6,
+      "k_max": 16,
+      "graph_k": 12,
+      "cross_patch_k": 8,
+      "density_gamma": 0.4,
+      "eta_max": 0.6,
+      "gamma_perp_max": 0.3,
+      "trust_floor": 0.35,
+      "trust_scale": 0.65,
+      "depth": 1,
+      "cross_patch": true,
+      "edge_dropout": 0.0,
+      "message_dropout": 0.0,
+      "residual_gate_init": -1.0,
+      "cross_patch_radius": 512.0,
+      "ct_same_type_only": true,
+      "ct_conf_min": 0.2,
+      "apply_to_embeddings": false,
+      "apply_to_ref_weights": false,
+      "apply_to_expr_residual": true,
+      "use_gt_ct": false,
+      "enabled": true,
+      "ablation_off": false
+    },
+    "vq_patch": {
+      "enabled": true,
+      "n_codes": 64,
+      "beta": 0.25,
+      "use_cosine": true,
+      "inject_cell": false,
+      "loss_w": 0.05
+    },
+    "ct_priors_ecrm_unit_enabled": true
+  },
+  "training": {
+    "batch_size": 64,
+    "total_epochs": 30,
+    "learning_rate": 0.00115,
+    "beta1": 0.9,
+    "beta2": 0.999,
+    "weight_decay": 0.00001,
+    "eps": 1E-8,
+    "stain_aug": true,
+    "uniform_sampler": true,
+    "immune_sampler_boost": 1.0,
+    "panel_completion_loss_weight": 0.0,
+    "panel_hide_frac": 0.0,
+    "panel_use_natural_missing": false,
+    "pearson_loss_weight": 0.0,
+    "expr_var_penalty_weight": 0.0,
+    "use_expr_baseline": false,
+    "holdout_n_genes": 0,
+    "batch_sampler_seed": 20260419,
+    "seed": 20260807
+  },
+  "evaluation": {
+    "parity_tolerance_abs": 0.001,
+    "external_source": "data_sources_test",
+    "external_every_epochs": 1,
+    "external_final_epoch": true
+  },
+  "save_freqs": {
+    "model_freq": 1
+  },
+  "experiment_dirs": {
+    "load_dir": "results",
+    "metrics_dir": "metrics",
+    "model_dir": "models"
+  },
+  "stain_norm": {
+    "norm_train": true,
+    "norm_val": true,
+    "norm_test": true,
+    "fp_norm_ref": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+    "resized_scale": 0.2
+  },
+  "data_sources_train_val": [
+    {
+      "slide_idx": 0,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 1,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast3/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 5,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast4/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 2,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast5/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 4,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast7/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/matched_nuclei_filtered.csv"
+    }
+  ],
+  "data_sources_test": [
+    {
+      "slide_idx": 6,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5k/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast_5k/aligned_he_image.tif",
+      "fp_expr": "",
+      "fp_cell_type": "",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5k/matched_nuclei_filtered.csv"
+    }
+  ]
+}

GHIST_plus/models/breast_multi/config_multi_breast.json

@@ -0,0 +1,182 @@
+{
+    "comps": {
+      "avgexp": true,
+      "celltype": true,
+      "crossattn": true,
+      "use_neighb": true,
+      "neighb": true
+    },
+    "regions_val": {"divisions": [[0.0, 0.2]]},
+    "regions_test": {"divisions": [[0.0, 1.0]]},
+    "data": {
+      "cell_types": [
+        "B",
+        "Myeloid (excluding macrophage)",
+        "Stromal",
+        "Macrophage",
+        "Malignant",
+        "Epithelial",
+        "Plasma",
+        "T",
+        "Unassigned"
+      ],
+      "min_nuc_area": 10,
+      "expr_scale": 2.0,
+      "foundation_model_input_normalization": "uni2_imagenet",
+      "num_workers": 32,
+      "hsize": 224,
+      "wsize": 224,
+      "overlap": 30,
+      "max_cells_per_patch": 2048,
+      "pin_memory": false
+    },
+    "model": {
+      "foundation_model": {
+        "enabled": true,
+        "pretrained": true,
+        "train_adapter": false
+      },
+      "emb_dim": 1024,
+      "avgexp_temp": 1.0,
+      "avgexp_residual_scale": 1.0,
+      "refiner_query_tokens": 8,
+      "hurdle": {
+        "enabled": true,
+        "sigma_init": 0.5,
+        "sigma_floor": 0.03
+      },
+      "ecrm": {
+        "k_target": 12,
+        "k_min": 6,
+        "k_max": 16,
+        "graph_k": 12,
+        "cross_patch_k": 8,
+        "density_gamma": 0.4,
+        "eta_max": 0.6,
+        "gamma_perp_max": 0.3,
+        "trust_floor": 0.35,
+        "trust_scale": 0.65,
+        "depth": 1,
+        "cross_patch": true,
+        "edge_dropout": 0.0,
+        "message_dropout": 0.0,
+        "residual_gate_init": -1.0,
+        "cross_patch_radius": 512.0,
+        "ct_same_type_only": true,
+        "ct_conf_min": 0.2,
+        "apply_to_embeddings": false,
+        "apply_to_ref_weights": false,
+        "apply_to_expr_residual": true,
+        "use_gt_ct": false,
+        "enabled": true,
+        "ablation_off": false
+      },
+      "vq_patch": {
+        "enabled": true,
+        "n_codes": 64,
+        "beta": 0.25,
+        "use_cosine": true,
+        "inject_cell": false,
+        "loss_w": 0.05
+      },
+      "ct_priors_ecrm_unit_enabled": true
+    },
+    "training": {
+      "batch_size": 64,
+      "total_epochs": 30,
+      "learning_rate": 0.00115,
+      "beta1": 0.9,
+      "beta2": 0.999,
+      "weight_decay": 0.00001,
+      "eps": 1e-08,
+      "stain_aug": true,
+      "uniform_sampler": true,
+      "immune_sampler_boost": 1.0,
+      "panel_completion_loss_weight": 0.0,
+      "panel_hide_frac": 0.0,
+      "panel_use_natural_missing": false,
+      "pearson_loss_weight": 0.0,
+      "expr_var_penalty_weight": 0.0,
+      "use_expr_baseline": false,
+      "holdout_n_genes": 0,
+      "batch_sampler_seed": 20260419,
+      "seed": 20260807
+    },
+    "evaluation": {
+      "parity_tolerance_abs": 0.001,
+      "external_source": "data_sources_test",
+      "external_every_epochs": 1,
+      "external_final_epoch": true
+    },
+    "save_freqs": {"model_freq": 1},
+    "experiment_dirs": {
+      "load_dir": "results",
+      "metrics_dir": "metrics",
+      "model_dir": "models"
+    },
+    "stain_norm": {
+      "norm_train": true,
+      "norm_val": true,
+      "norm_test": true,
+      "fp_norm_ref": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+      "resized_scale": 0.2
+    },
+    "data_sources_train_val": [
+      {
+        "slide_idx": 0,
+        "domain_id": 0,
+        "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/he_image_nuclei_seg.tif",
+        "fp_hist": "${GHIST_DATA_ROOT}/breast/aligned_he_image.tif",
+        "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_gene_matrix_filtered.csv",
+        "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_type_filtered.csv",
+        "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/matched_nuclei_filtered.csv"
+      },
+      {
+        "slide_idx": 1,
+        "domain_id": 0,
+        "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/he_image_nuclei_seg.tif",
+        "fp_hist": "${GHIST_DATA_ROOT}/breast3/aligned_he_image.tif",
+        "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_gene_matrix_filtered.csv",
+        "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_type_filtered.csv",
+        "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/matched_nuclei_filtered.csv"
+      },
+      {
+        "slide_idx": 5,
+        "domain_id": 0,
+        "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/he_image_nuclei_seg.tif",
+        "fp_hist": "${GHIST_DATA_ROOT}/breast4/aligned_he_image.tif",
+        "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_gene_matrix_filtered.csv",
+        "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_type_filtered.csv",
+        "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/matched_nuclei_filtered.csv"
+      },
+      {
+        "slide_idx": 2,
+        "domain_id": 0,
+        "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/he_image_nuclei_seg.tif",
+        "fp_hist": "${GHIST_DATA_ROOT}/breast5/aligned_he_image.tif",
+        "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_gene_matrix_filtered.csv",
+        "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_type_filtered.csv",
+        "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/matched_nuclei_filtered.csv"
+      },
+      {
+        "slide_idx": 4,
+        "domain_id": 0,
+        "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/he_image_nuclei_seg.tif",
+        "fp_hist": "${GHIST_DATA_ROOT}/breast7/aligned_he_image.tif",
+        "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_gene_matrix_filtered.csv",
+        "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_type_filtered.csv",
+        "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/matched_nuclei_filtered.csv"
+      }
+    ],
+    "data_sources_test": [
+      {
+        "slide_idx": 3,
+        "domain_id": 0,
+        "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image_nuclei_seg.tif",
+        "fp_hist": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+        "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_gene_matrix_filtered.csv",
+        "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_type_filtered.csv",
+        "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/matched_nuclei_filtered.csv"
+      }
+    ]
+  }

GHIST_plus/models/breast_multi/genes.txt

@@ -0,0 +1,413 @@
+ABCC11
+ACKR1
+ACTA2
+ACTG2
+ADAM9
+ADGRE5
+ADGRL4
+ADH1B
+ADIPOQ
+AEBP1
+AGR3
+AHSP
+AIF1
+AKR1C1
+AKR1C3
+ALDH1A3
+ANGPT2
+ANKRD28
+ANKRD29
+ANKRD30A
+APC
+APOBEC3A
+APOBEC3B
+APOC1
+AQP1
+AQP3
+AR
+ARSG
+AVPR1A
+BAALC
+BACE2
+BANK1
+BASP1
+BIRC3
+BTNL9
+BUB1
+C1QA
+C1QC
+C2orf42
+C5orf46
+C6orf132
+C11orf96
+C15orf48
+CACNG4
+CAPN9
+CAV1
+CAVIN2
+CCDC6
+CCDC80
+CCL5
+CCL8
+CCL18
+CCL19
+CCL20
+CCL26
+CCND1
+CCPG1
+CCR7
+CD1C
+CD3D
+CD3E
+CD3G
+CD4
+CD8A
+CD8B
+CD9
+CD14
+CD19
+CD27
+CD36
+CD40
+CD52
+CD68
+CD69
+CD79A
+CD79B
+CD80
+CD83
+CD86
+CD93
+CD96
+CD163
+CD247
+CD274
+CDC42EP1
+CDH1
+CEACAM6
+CEACAM8
+CEBPB
+CEL
+CENPF
+CILP
+CLCA2
+CLDN4
+CLDN5
+CLEC9A
+CLEC14A
+CLECL1
+CLIC6
+CPA3
+CRHBP
+CRISPLD2
+CSF3
+CST1
+CTH
+CTHRC1
+CTLA4
+CTSG
+CTTN
+CX3CR1
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+CXCL9
+CXCL12
+CXCL16
+CXCR3
+CXCR4
+CYP1A1
+CYTIP
+DAPK3
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+EGFR
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+EPHA4
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+FAM49A
+FAM107B
+FASN
+FBLIM1
+FBLN1
+FBLN2
+FCER1A
+FCER1G
+FCGR3A
+FGFR1
+FGL2
+FLNB
+FOSL1
+FOXA1
+FOXC2
+FOXP3
+FSTL3
+G0S2
+GABRP
+GATA3
+GJB2
+GLIPR1
+GNLY
+GPR183
+GPX3
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+GZMA
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+GZMK
+HAVCR2
+HDC
+HMGA1
+HMGCS2
+HOOK2
+HOXD8
+HOXD9
+HPX
+ID4
+IFNB1
+IGF1
+IGF1R
+IGFBP6
+IGSF6
+IL2RA
+IL2RG
+IL3RA
+IL4
+IL7R
+IL17A
+IL22
+IL23A
+IL32
+INHBA
+IQCJ
+ISLR
+ITGAM
+ITGAX
+ITGB1
+ITM2C
+JUP
+KARS
+KDR
+KIT
+KLF5
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+KLRD1
+KLRF1
+KRT5
+KRT6B
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+KRT8
+KRT14
+KRT15
+KRT16
+KRT23
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+LARS
+LDHA
+LDHB
+LEF1
+LEP
+LGALS9
+LGALSL
+LIF
+LILRA4
+LPL
+LPXN
+LRRC15
+LRRC31
+LTB
+LUM
+LY86
+LYPD3
+LYZ
+MAP3K8
+MCM6
+MDM2
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+MFAP4
+MFAP5
+MKI67
+MLPH
+MMP1
+MMP2
+MMP11
+MMP12
+MMRN2
+MNDA
+MPO
+MRC1
+MS4A1
+MUC1
+MUC5B
+MUC6
+MYBPC1
+MYH11
+MYLK
+MYO5B
+MZB1
+NARS
+NCAM1
+NDUFA4L2
+NKG7
+NLRC5
+NNMT
+NOSTRIN
+NPM3
+NXPH1
+OCIAD2
+OPRPN
+OXTR
+PCDH10
+PCLAF
+PCOLCE
+PDCD1
+PDCD1LG2
+PDE4A
+PDGFRA
+PDGFRB
+PDK4
+PDZK1
+PECAM1
+PELI1
+PGR
+PIGR
+PIK3CG
+PIM1
+PLD4
+PLIN1
+PLK1
+POLR2J3
+POSTN
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+PRDM1
+PRF1
+PTGDS
+PTN
+PTPRC
+PTRHD1
+QARS
+RAB30
+RAMP2
+RAPGEF3
+RARRES2
+REXO4
+RGS5
+RHOH
+ROR1
+RORC
+RTKN2
+RUNX1
+S100A4
+S100A8
+S100A14
+SCD
+SCGB2A1
+SDC4
+SEC11C
+SEC24A
+SELL
+SERHL2
+SERPINA3
+SERPINB9
+SERPING1
+SFRP1
+SFRP4
+SH3YL1
+SLAMF1
+SLAMF7
+SLC4A1
+SLC5A6
+SLC25A37
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+SMAP2
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+SNX20
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+SRGN
+SRPK1
+SSTR2
+STAT3
+STC1
+STC2
+SVIL
+TAC1
+TACSTD2
+TAP1
+TAPBP
+TBX3
+TCEAL7
+TCF4
+TCF7
+TCF15
+TCIM
+TCL1A
+TENT5C
+TFAP2A
+TGFBR1
+THAP2
+THBS2
+THY1
+TIFA
+TIGIT
+TIMP4
+TMEM147
+TNFRSF17
+TNS4
+TNXB
+TOMM7
+TOP2A
+TPD52
+TPSAB1
+TRAC
+TRAF4
+TRAPPC3
+TRAT1
+TRBC1
+TRH
+TRIB1
+TSPAN8
+TUBA4A
+TUBB2B
+TYROBP
+UBD
+UCP1
+USP53
+VEGFC
+VOPP1
+VWF
+WARS
+XCR1
+ZEB1
+ZEB2
+ZNF562

GHIST_plus/models/breast_multi/ghist_plus_breast_multi_checkpoint.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:b0194f6d6736c8c65cced7b65db0013d1ba61484345c3ea9855393a60018637e
+size 184217730

GHIST_plus/models/breast_multi/ghist_plus_breast_multi_optimizer.pth

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+version https://git-lfs.github.com/spec/v1
+oid sha256:8500b17395a2d09546966dad1601d0e66dd1484f244e8d98255da969b8f1a50f
+size 173521230

GHIST_plus/models/breast_multi/standardisation_hist_fold_1.npy

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+version https://git-lfs.github.com/spec/v1
+oid sha256:3f172e9742c1ceb7783b1187e9900d8a51f67e2322a85ca441b0a9621dcf5e79
+size 176

GHIST_plus/models/breast_single/config.json

@@ -0,0 +1,148 @@
+{
+  "comps": {
+    "avgexp": true,
+    "celltype": true,
+    "crossattn": true,
+    "use_neighb": true,
+    "neighb": true
+  },
+  "regions_val": {
+    "divisions": [
+      [
+        0.0,
+        0.2
+      ]
+    ]
+  },
+  "data": {
+    "cell_types": [
+      "B",
+      "Myeloid (excluding macrophage)",
+      "Stromal",
+      "Macrophage",
+      "Malignant",
+      "Epithelial",
+      "Plasma",
+      "T",
+      "Unassigned"
+    ],
+    "min_nuc_area": 10,
+    "expr_scale": 2.0,
+    "foundation_model_input_normalization": "uni2_imagenet",
+    "num_workers": 24,
+    "hsize": 224,
+    "wsize": 224,
+    "overlap": 30,
+    "max_cells_per_patch": 2048,
+    "pin_memory": false
+  },
+  "model": {
+    "foundation_model": {
+      "enabled": true,
+      "pretrained": true,
+      "train_adapter": false
+    },
+    "emb_dim": 1024,
+    "avgexp_temp": 1.0,
+    "avgexp_residual_scale": 1.0,
+    "refiner_query_tokens": 8,
+    "hurdle": {
+      "enabled": true,
+      "sigma_init": 0.5,
+      "sigma_floor": 0.03
+    },
+    "ecrm": {
+      "k_target": 12,
+      "k_min": 6,
+      "k_max": 16,
+      "graph_k": 12,
+      "cross_patch_k": 8,
+      "density_gamma": 0.4,
+      "eta_max": 0.6,
+      "gamma_perp_max": 0.3,
+      "trust_floor": 0.35,
+      "trust_scale": 0.65,
+      "depth": 1,
+      "cross_patch": true,
+      "edge_dropout": 0.0,
+      "message_dropout": 0.0,
+      "residual_gate_init": -1.0,
+      "cross_patch_radius": 512.0,
+      "ct_same_type_only": true,
+      "ct_conf_min": 0.2,
+      "apply_to_embeddings": false,
+      "apply_to_ref_weights": false,
+      "apply_to_expr_residual": true,
+      "use_gt_ct": false,
+      "enabled": true,
+      "ablation_off": false
+    },
+    "vq_patch": {
+      "enabled": true,
+      "n_codes": 64,
+      "beta": 0.25,
+      "use_cosine": true,
+      "inject_cell": false,
+      "loss_w": 0.05
+    },
+    "ct_priors_ecrm_unit_enabled": true
+  },
+  "training": {
+    "batch_size": 64,
+    "total_epochs": 30,
+    "learning_rate": 0.00115,
+    "beta1": 0.9,
+    "beta2": 0.999,
+    "weight_decay": 0.00001,
+    "eps": 1E-8,
+    "stain_aug": true,
+    "uniform_sampler": true,
+    "immune_sampler_boost": 1.0,
+    "panel_completion_loss_weight": 0.0,
+    "panel_hide_frac": 0.0,
+    "panel_use_natural_missing": false,
+    "pearson_loss_weight": 0.0,
+    "expr_var_penalty_weight": 0.0,
+    "use_expr_baseline": false,
+    "holdout_n_genes": 0,
+    "batch_sampler_seed": 20260419,
+    "seed": 20260807
+  },
+  "evaluation": {
+    "parity_tolerance_abs": 0.001,
+    "external_source": "data_sources_train_val"
+  },
+  "save_freqs": {
+    "model_freq": 1
+  },
+  "experiment_dirs": {
+    "load_dir": "results",
+    "metrics_dir": "metrics",
+    "model_dir": "models"
+  },
+  "stain_norm": {
+    "norm_train": false,
+    "norm_val": false,
+    "norm_test": false,
+    "fp_norm_ref": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+    "resized_scale": 0.2
+  },
+  "data_sources_train_val": [
+    {
+      "slide_idx": 3,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/matched_nuclei_filtered.csv",
+      "cell_coords_id_space": "histology",
+      "cell_coords_validate_alignment": true,
+      "cell_coords_alignment_sample_size": 256,
+      "cell_coords_alignment_tolerance_px": 1.0,
+      "cell_coords_alignment_window_radius_px": 64
+    }
+  ],
+  "data_sources_test": [],
+  "run_label": "breast2_ablation9_full"
+}

GHIST_plus/models/breast_single/genes.txt

@@ -0,0 +1,280 @@
+ABCC11
+ACTA2
+ACTG2
+ADAM9
+ADGRE5
+ADH1B
+ADIPOQ
+AGR3
+AIF1
+AKR1C1
+AKR1C3
+ALDH1A3
+ANGPT2
+ANKRD28
+ANKRD29
+ANKRD30A
+APOBEC3A
+APOBEC3B
+APOC1
+AQP1
+AQP3
+AR
+AVPR1A
+BACE2
+BANK1
+BASP1
+C1QA
+C1QC
+C2orf42
+C5orf46
+C6orf132
+C15orf48
+CAV1
+CAVIN2
+CCDC6
+CCDC80
+CCL5
+CCL8
+CCND1
+CCPG1
+CCR7
+CD3E
+CD3G
+CD4
+CD8A
+CD9
+CD14
+CD19
+CD27
+CD68
+CD69
+CD79A
+CD79B
+CD80
+CD83
+CD86
+CD93
+CD163
+CD247
+CD274
+CDC42EP1
+CDH1
+CEACAM6
+CEACAM8
+CENPF
+CLEC9A
+CLEC14A
+CLECL1
+CLIC6
+CPA3
+CRISPLD2
+CTH
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GHIST_plus/models/breast_single/ghist_plus_breast_single_optimizer.pth

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GHIST_plus/models/breast_single/standardisation_hist_fold_1.npy

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GHIST_plus/models/imputation/config_gene_mask_imputer.json

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+{
+    "comps": {
+        "avgexp": true,
+        "celltype": true,
+        "crossattn": true,
+        "use_neighb": true,
+        "neighb": true
+    },
+    "stain_norm": {
+        "norm_train": true,
+        "norm_val": true,
+        "norm_test": true,
+        "fp_norm_ref": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+        "resized_scale": 0.2
+    },
+    "regions_val": {
+        "divisions": [
+            [
+                0.0,
+                0.2
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+            [
+                0.0,
+                1.0
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+        ]
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+    "data": {
+        "cell_types": [
+            "B",
+            "Myeloid (excluding macrophage)",
+            "Stromal",
+            "Macrophage",
+            "Malignant",
+            "Epithelial",
+            "Plasma",
+            "T",
+            "Unassigned"
+        ],
+        "min_nuc_area": 10,
+        "expr_scale": 2.0,
+        "foundation_model_input_normalization": "uni2_imagenet",
+        "num_workers": 32,
+        "hsize": 224,
+        "wsize": 224,
+        "overlap": 30,
+        "max_cells_per_patch": 2048,
+        "pin_memory": false
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+            "train_adapter": false
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+        "avgexp_temp": 1.0,
+        "avgexp_residual_scale": 1.0,
+        "refiner_query_tokens": 8,
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+            "density_gamma": 0.4,
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+            "ct_same_type_only": true,
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+            "apply_to_ref_weights": false,
+            "apply_to_expr_residual": true,
+            "use_gt_ct": false,
+            "enabled": true,
+            "ablation_off": false
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+        "vq_patch": {
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+            "n_codes": 64,
+            "beta": 0.25,
+            "use_cosine": true,
+            "inject_cell": false,
+            "loss_w": 0.05
+        },
+        "ct_priors_ecrm_unit_enabled": true
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+    "gene_mask_imputer": {
+        "enabled": true,
+        "mask_n_genes": 10,
+        "mask_strategy": "fixed_giotto_csv_per_slide",
+        "svg_knn_k": 8,
+        "svg_sample_cap": 3000,
+        "fixed_gene_csv_dir": "configs/gene_mask_imputer_fixed_giotto",
+        "create_fixed_gene_csv_if_missing": true,
+        "random_mask_frac": 0.3,
+        "use_morph": true,
+        "copy_observed": true,
+        "mask_seed": 0
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+    "training": {
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+        "total_epochs": 30,
+        "learning_rate": 0.00115,
+        "beta1": 0.9,
+        "beta2": 0.999,
+        "weight_decay": 1e-05,
+        "eps": 1e-08,
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+        "pearson_loss_weight": 0.0,
+        "expr_var_penalty_weight": 0.0,
+        "use_expr_baseline": false,
+        "holdout_n_genes": 0,
+        "batch_sampler_seed": 20260419,
+        "seed": 20260807
+    },
+    "evaluation": {
+        "parity_tolerance_abs": 0.001,
+        "external_source": "data_sources_test",
+        "external_every_epochs": 1,
+        "external_final_epoch": true
+    },
+    "save_freqs": {
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+    },
+    "data_sources_train_val": [
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+            "domain_id": 0,
+            "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/he_image_nuclei_seg.tif",
+            "fp_hist": "${GHIST_DATA_ROOT}/breast/aligned_he_image.tif",
+            "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_gene_matrix_filtered.csv",
+            "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_type_filtered.csv",
+            "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/matched_nuclei_filtered.csv"
+        },
+        {
+            "slide_idx": 1,
+            "domain_id": 0,
+            "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/he_image_nuclei_seg.tif",
+            "fp_hist": "${GHIST_DATA_ROOT}/breast3/aligned_he_image.tif",
+            "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_gene_matrix_filtered.csv",
+            "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_type_filtered.csv",
+            "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/matched_nuclei_filtered.csv"
+        },
+        {
+            "slide_idx": 5,
+            "domain_id": 0,
+            "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/he_image_nuclei_seg.tif",
+            "fp_hist": "${GHIST_DATA_ROOT}/breast4/aligned_he_image.tif",
+            "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_gene_matrix_filtered.csv",
+            "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_type_filtered.csv",
+            "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/matched_nuclei_filtered.csv"
+        },
+        {
+            "slide_idx": 2,
+            "domain_id": 0,
+            "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/he_image_nuclei_seg.tif",
+            "fp_hist": "${GHIST_DATA_ROOT}/breast5/aligned_he_image.tif",
+            "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_gene_matrix_filtered.csv",
+            "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_type_filtered.csv",
+            "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/matched_nuclei_filtered.csv"
+        },
+        {
+            "slide_idx": 4,
+            "domain_id": 0,
+            "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/he_image_nuclei_seg.tif",
+            "fp_hist": "${GHIST_DATA_ROOT}/breast7/aligned_he_image.tif",
+            "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_gene_matrix_filtered.csv",
+            "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_type_filtered.csv",
+            "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/matched_nuclei_filtered.csv"
+        }
+    ],
+    "data_sources_test": [
+        {
+            "slide_idx": 3,
+            "domain_id": 0,
+            "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image_nuclei_seg.tif",
+            "fp_hist": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+            "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_gene_matrix_filtered.csv",
+            "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_type_filtered.csv",
+            "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/matched_nuclei_filtered.csv"
+        }
+    ],
+    "experiment_dirs": {
+        "load_dir": "results",
+        "metrics_dir": "metrics",
+        "model_dir": "models"
+    }
+}

GHIST_plus/models/imputation/genes.txt

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+ABCC11
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GHIST_plus/models/imputation/ghist_plus_gene_imputation_checkpoint.pth

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GHIST_plus/models/imputation/ghist_plus_gene_imputation_optimizer.pth

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+size 176071174

GHIST_plus/models/imputation/holdout_genes_by_slide.json

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+{
+  "genes_by_slide": {
+    "0": [
+      "ANKRD30A",
+      "CCND1",
+      "CEACAM6",
+      "EPCAM",
+      "ERBB2",
+      "FASN",
+      "FOXA1",
+      "GATA3",
+      "KRT7",
+      "SCD"
+    ],
+    "1": [
+      "CLIC6",
+      "GATA3",
+      "KRT14",
+      "MUC1",
+      "MYBPC1",
+      "MYH11",
+      "PGR",
+      "SERPINA3",
+      "SFRP1",
+      "TPD52"
+    ],
+    "2": [
+      "ADH1B",
+      "CCDC80",
+      "CXCL12",
+      "FASN",
+      "FOXA1",
+      "GATA3",
+      "KRT7",
+      "SCD",
+      "TACSTD2",
+      "TPD52"
+    ],
+    "4": [
+      "CCDC80",
+      "CXCL12",
+      "EGR1",
+      "GATA3",
+      "KRT7",
+      "MUC1",
+      "SCD",
+      "SERPING1",
+      "STC2",
+      "TPD52"
+    ],
+    "5": [
+      "CLIC6",
+      "FASN",
+      "GATA3",
+      "KRT14",
+      "LYZ",
+      "MYBPC1",
+      "PGR",
+      "SERPINA3",
+      "SFRP1",
+      "TPD52"
+    ]
+  },
+  "holdout_hash": "defb72b6",
+  "mask_n_genes": 10,
+  "mask_strategy": "fixed_giotto_csv_per_slide",
+  "svg_knn_k": 8,
+  "svg_sample_cap": 3000,
+  "task_name": "gene_mask_imputer"
+}

GHIST_plus/models/imputation/standardisation_hist_fold_1.npy

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+version https://git-lfs.github.com/spec/v1
+oid sha256:3f172e9742c1ceb7783b1187e9900d8a51f67e2322a85ca441b0a9621dcf5e79
+size 176

GHIST_plus/models/pancancer/config.json

@@ -0,0 +1,280 @@
+{
+  "comps": {
+    "avgexp": true,
+    "celltype": true,
+    "crossattn": true,
+    "use_neighb": true,
+    "neighb": true
+  },
+  "regions_val": {
+    "divisions": [
+      [
+        0.0,
+        0.2
+      ]
+    ]
+  },
+  "data": {
+    "cell_types": [
+      "B",
+      "Myeloid (excluding macrophage)",
+      "Stromal",
+      "Macrophage",
+      "Malignant",
+      "Epithelial",
+      "Plasma",
+      "T",
+      "Unassigned"
+    ],
+    "min_nuc_area": 10,
+    "expr_scale": 2.0,
+    "foundation_model_input_normalization": "uni2_imagenet",
+    "num_workers": 24,
+    "hsize": 224,
+    "wsize": 224,
+    "overlap": 30,
+    "max_cells_per_patch": 2048,
+    "pin_memory": false
+  },
+  "model": {
+    "foundation_model": {
+      "enabled": true,
+      "pretrained": true,
+      "train_adapter": false
+    },
+    "emb_dim": 1024,
+    "avgexp_temp": 1.0,
+    "avgexp_residual_scale": 1.0,
+    "refiner_query_tokens": 8,
+    "hurdle": {
+      "enabled": true,
+      "sigma_init": 0.5,
+      "sigma_floor": 0.03
+    },
+    "ecrm": {
+      "k_target": 12,
+      "k_min": 6,
+      "k_max": 16,
+      "graph_k": 12,
+      "cross_patch_k": 8,
+      "density_gamma": 0.4,
+      "eta_max": 0.6,
+      "gamma_perp_max": 0.3,
+      "trust_floor": 0.35,
+      "trust_scale": 0.65,
+      "depth": 1,
+      "cross_patch": true,
+      "edge_dropout": 0.0,
+      "message_dropout": 0.0,
+      "residual_gate_init": -1.0,
+      "cross_patch_radius": 512.0,
+      "ct_same_type_only": true,
+      "ct_conf_min": 0.2,
+      "apply_to_embeddings": false,
+      "apply_to_ref_weights": false,
+      "apply_to_expr_residual": true,
+      "use_gt_ct": false,
+      "enabled": true,
+      "ablation_off": false
+    },
+    "vq_patch": {
+      "enabled": true,
+      "n_codes": 64,
+      "beta": 0.25,
+      "use_cosine": true,
+      "inject_cell": false,
+      "loss_w": 0.05
+    },
+    "ct_priors_ecrm_unit_enabled": true
+  },
+  "training": {
+    "batch_size": 64,
+    "total_epochs": 30,
+    "learning_rate": 0.00115,
+    "beta1": 0.9,
+    "beta2": 0.999,
+    "weight_decay": 1e-05,
+    "eps": 1e-08,
+    "stain_aug": true,
+    "uniform_sampler": true,
+    "immune_sampler_boost": 1.0,
+    "panel_completion_loss_weight": 0.0,
+    "panel_hide_frac": 0.0,
+    "panel_use_natural_missing": false,
+    "pearson_loss_weight": 0.0,
+    "expr_var_penalty_weight": 0.0,
+    "use_expr_baseline": false,
+    "holdout_n_genes": 0,
+    "batch_sampler_seed": 20260419,
+    "seed": 20260807
+  },
+  "evaluation": {
+    "internal_validation": false,
+    "parity_tolerance_abs": 0.001,
+    "external_source": "data_sources_test",
+    "external_every_epochs": 1,
+    "external_final_epoch": true
+  },
+  "save_freqs": {
+    "model_freq": 1
+  },
+  "experiment_dirs": {
+    "load_dir": "results",
+    "metrics_dir": "metrics",
+    "model_dir": "models"
+  },
+  "stain_norm": {
+    "norm_train": false,
+    "norm_val": false,
+    "norm_test": false,
+    "fp_norm_ref": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+    "resized_scale": 0.2
+  },
+  "data_sources_train_val": [
+    {
+      "slide_idx": 0,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/pancreas/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas/cell_gene_matrix_380_aligned.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 1,
+      "domain_id": 1,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/colorectal/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal/cell_gene_matrix_380_aligned.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 2,
+      "domain_id": 3,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/lung/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 3,
+      "domain_id": 2,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast2/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 4,
+      "domain_id": 3,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung2/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/lung2/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung2/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung2/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung2/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 5,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas2/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/pancreas2/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas2/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas2/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas2/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 6,
+      "domain_id": 1,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal2/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/colorectal2/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal2/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal2/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal2/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 7,
+      "domain_id": 2,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 8,
+      "domain_id": 2,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast3/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast3/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 9,
+      "domain_id": 2,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast4/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast4/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 10,
+      "domain_id": 2,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast5/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast5/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 12,
+      "domain_id": 3,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung3/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/lung3/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung3/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung3/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_lung3/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 13,
+      "domain_id": 2,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/breast7/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_breast7/matched_nuclei_filtered.csv"
+    },
+    {
+      "slide_idx": 15,
+      "domain_id": 1,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal3/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/colorectal3/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal3/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal3/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_colorectal3/matched_nuclei_filtered.csv"
+    }
+  ],
+  "data_sources_test": [
+    {
+      "slide_idx": 14,
+      "domain_id": 0,
+      "fp_nuc_seg": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas3/he_image_nuclei_seg.tif",
+      "fp_hist": "${GHIST_DATA_ROOT}/pancreas3/aligned_he_image.tif",
+      "fp_expr": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas3/cell_gene_matrix_filtered.csv",
+      "fp_cell_type": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas3/cell_type_filtered.csv",
+      "fp_nuc_sizes": "${GHIST_DATA_ROOT}/data_processing/data_processing_pancreas3/matched_nuclei_filtered.csv"
+    }
+  ],
+  "regions_test": {
+    "divisions": [
+      [
+        0.0,
+        0.2
+      ]
+    ]
+  }
+}

GHIST_plus/models/pancancer/genes.txt

@@ -0,0 +1,1275 @@
+A2M
+ABCA8
+ABCC8
+ABCC11
+ACACB
+ACE
+ACE2
+ACKR1
+ACTA2
+ACTB
+ACTG2
+ACTN1
+ADAM9
+ADAM17
+ADAM28
+ADAMTS1
+ADGRE1
+ADGRE5
+ADGRL4
+ADH1B
+ADH1C
+ADH4
+ADIPOQ
+ADRA2A
+AEBP1
+AFAP1L2
+AGER
+AGR3
+AGTR1
+AHSP
+AIF1
+AIRE
+AKR1C1
+AKR1C3
+AKR7A3
+AKT1
+ALAS2
+ALDH1A3
+ALDH1B1
+ALOX5AP
+AMY2A
+ANGPT2
+ANK2
+ANKRD28
+ANKRD29
+ANKRD30A
+ANO7
+ANPEP
+ANXA1
+ANXA3
+ANXA13
+APC
+APCDD1
+APOA5
+APOB
+APOBEC3A
+APOBEC3B
+APOC1
+APOD
+APOE
+APOLD1
+AQP1
+AQP2
+AQP3
+AQP8
+AQP9
+AR
+AREG
+ARFGEF3
+ARG1
+ARHGAP24
+ARID1A
+ARL14
+ARPC3
+ARPC5
+ARSG
+ARX
+ASAH1
+ASCL1
+ASCL2
+ASCL3
+ASPN
+ATM
+ATOH1
+ATP1B1
+ATP5F1B
+ATP5MC2
+ATP5MD
+AVIL
+AVPR1A
+AZGP1
+B3GNT6
+BAALC
+BACE2
+BAIAP2L1
+BAMBI
+BANK1
+BASP1
+BATF
+BATF3
+BBOX1
+BCAS1
+BCL2
+BCL2L11
+BEST2
+BEST4
+BIRC3
+BMP4
+BMP5
+BMX
+BRAF
+BRCA2
+BTF3
+BTNL9
+BUB1
+C1QA
+C1QB
+C1QBP
+C1QC
+C1R
+C1S
+C1orf162
+C1orf194
+C2orf42
+C2orf88
+C5orf46
+C6orf118
+C6orf132
+C7
+C11orf96
+C15orf48
+C20orf85
+CA1
+CA2
+CA4
+CA7
+CACNG4
+CADM2
+CADPS
+CALB2
+CALU
+CAP1
+CAPN8
+CAPN9
+CAST
+CAV1
+CAVIN1
+CAVIN2
+CCDC6
+CCDC39
+CCDC78
+CCDC80
+CCL2
+CCL3
+CCL3L1
+CCL4
+CCL5
+CCL7
+CCL8
+CCL11
+CCL13
+CCL14
+CCL15
+CCL16
+CCL18
+CCL19
+CCL20
+CCL21
+CCL26
+CCL27
+CCL28
+CCNA1
+CCNB2
+CCND1
+CCPG1
+CCR1
+CCR2
+CCR3
+CCR4
+CCR5
+CCR6
+CCR7
+CD1A
+CD1C
+CD1E
+CD2
+CD3D
+CD3E
+CD3G
+CD4
+CD5
+CD5L
+CD6
+CD7
+CD8A
+CD8B
+CD9
+CD14
+CD19
+CD24
+CD27
+CD28
+CD34
+CD36
+CD37
+CD38
+CD40
+CD40LG
+CD44
+CD47
+CD52
+CD68
+CD69
+CD70
+CD74
+CD79A
+CD79B
+CD80
+CD83
+CD86
+CD93
+CD96
+CD163
+CD177
+CD247
+CD274
+CD276
+CD300E
+CDC42EP1
+CDCA7
+CDH1
+CDH16
+CDH19
+CDHR5
+CDK1
+CDK2
+CDK4
+CDK6
+CDK12
+CDK15
+CDKN1A
+CDKN1B
+CDKN1C
+CDKN2A
+CDKN2B
+CDKN2C
+CDKN2D
+CDX1
+CDX2
+CEACAM1
+CEACAM5
+CEACAM6
+CEACAM7
+CEACAM8
+CEBPB
+CEL
+CENPF
+CENPV
+CEP126
+CES1
+CES2
+CFAP53
+CFB
+CFC1
+CFHR1
+CFHR3
+CFTR
+CHGA
+CHGB
+CHI3L2
+CHIT1
+CHP2
+CHRM3
+CIB1
+CILP
+CKAP4
+CLCA1
+CLCA2
+CLCA4
+CLDN4
+CLDN5
+CLEC4E
+CLEC9A
+CLEC10A
+CLEC12A
+CLEC14A
+CLECL1
+CLIC6
+CLU
+CMA1
+CMBL
+CMKLR1
+CNN1
+CNN3
+COCH
+COL1A1
+COL5A2
+COL8A1
+COL11A1
+COL17A1
+COL19A1
+COMMD6
+CORO1A
+COTL1
+CP
+CPA3
+CPE
+CR2
+CREB3L1
+CRHBP
+CRISPLD2
+CRYBA2
+CSF1
+CSF1R
+CSF2RA
+CSF3
+CSPG4
+CST1
+CST7
+CSTA
+CTH
+CTHRC1
+CTLA4
+CTNNB1
+CTSB
+CTSD
+CTSE
+CTSG
+CTSK
+CTSL
+CTSS
+CTSW
+CTTN
+CX3CR1
+CXCL1
+CXCL2
+CXCL3
+CXCL5
+CXCL6
+CXCL9
+CXCL10
+CXCL11
+CXCL12
+CXCL13
+CXCL14
+CXCL16
+CXCR1
+CXCR2
+CXCR3
+CXCR4
+CXCR5
+CXCR6
+CYB5R3
+CYBB
+CYP1A1
+CYP2A7
+CYP2B6
+CYP2F1
+CYP3A4
+CYP4B1
+CYTIP
+DAPK2
+DAPK3
+DCLK1
+DCN
+DEPP1
+DERL3
+DES
+DGKA
+DGKG
+DHRS2
+DIO2
+DIRAS3
+DKK3
+DLK1
+DMBT1
+DMKN
+DNAAF1
+DNAJB9
+DNAJC12
+DNASE1L3
+DNTTIP1
+DOCK10
+DPEP1
+DPP6
+DPT
+DPYSL3
+DSC2
+DSP
+DST
+DUOX1
+DUOX2
+DUSP1
+DUSP2
+DUSP5
+E2F1
+EBPL
+ECM1
+ECSCR
+EDN1
+EDNRB
+EEF1B2
+EEF1D
+EFEMP1
+EGF
+EGFL7
+EGFR
+EGR1
+EGR3
+EHF
+EIF2S2
+EIF4A1
+EIF4EBP1
+ELF3
+ELF5
+ELOVL5
+EMP3
+ENAH
+ENTPD1
+EOMES
+EPAS1
+EPCAM
+EPHA2
+EPHA4
+EPHB3
+EPO
+EPOR
+ERBB2
+ERBB3
+ERBB4
+ERG
+ERN1
+ESM1
+ESR1
+ETS1
+ETV1
+ETV5
+F3
+FABP2
+FABP3
+FADD
+FAM3B
+FAM49A
+FAM107B
+FAM184A
+FAS
+FASLG
+FASN
+FBLIM1
+FBLN1
+FBLN2
+FBN1
+FCER1A
+FCER1G
+FCER2
+FCGR1A
+FCGR2A
+FCGR2B
+FCGR3A
+FCMR
+FCN1
+FCN2
+FCN3
+FCRL1
+FCRL3
+FCRLA
+FERMT1
+FEV
+FEZ1
+FFAR4
+FGF2
+FGFBP1
+FGFBP2
+FGFR1
+FGFR4
+FGL2
+FGR
+FHIT
+FHL1
+FHL2
+FKBP11
+FLNA
+FLNB
+FLT1
+FLT3LG
+FN1
+FOS
+FOSL1
+FOXA1
+FOXA3
+FOXC2
+FOXI1
+FOXJ1
+FOXP3
+FRZB
+FSCN1
+FSTL1
+FSTL3
+FXYD2
+FXYD5
+FYB1
+FZD7
+G0S2
+GABRP
+GADD45A
+GALNT5
+GALNT8
+GATA2
+GATA3
+GATM
+GCG
+GDF15
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