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batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 400 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151509/default.yaml b/spatialLIBD/151509/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2f6dc8f96ec53abbf75116072fcb532044145954 --- /dev/null +++ b/spatialLIBD/151509/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151509/processed_151509.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 400 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151510/default.yaml b/spatialLIBD/151510/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8a9634039f4ffd8a4da6b5791992a0cdf06b5abb --- /dev/null +++ b/spatialLIBD/151510/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151510/processed_151510.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 400 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151669/default.yaml b/spatialLIBD/151669/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1e003ded883366d3ea9b54b08fc019d2476722dd --- /dev/null +++ b/spatialLIBD/151669/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151669/processed_151669.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 300 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151670/default.yaml b/spatialLIBD/151670/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b54d845d513aaa1423f00cdd64536dc014a0fbf7 --- /dev/null +++ b/spatialLIBD/151670/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151670/processed_151670.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 400 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151671/default.yaml b/spatialLIBD/151671/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..925f2dace0472fd9282472d093f3cc183d8f1905 --- /dev/null +++ b/spatialLIBD/151671/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151671/processed_151671.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 200 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151672/default.yaml b/spatialLIBD/151672/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..b0ca59f5e3059f9971eabd77435205a50d7b538a --- /dev/null +++ b/spatialLIBD/151672/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151672/processed_151672.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 400 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151673/default.yaml b/spatialLIBD/151673/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2d382094073ab5e817492ee2c8a43fe0344b9cd9 --- /dev/null +++ b/spatialLIBD/151673/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151673/processed_151673.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 200 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151674/default.yaml b/spatialLIBD/151674/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9721a87c0ccf00deca831b67becb3338bbb7313c --- /dev/null +++ b/spatialLIBD/151674/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151674/processed_151674.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 300 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151675/default.yaml b/spatialLIBD/151675/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c6034c95f3b8c1f6eb7c93b431cbfeb1ec583d71 --- /dev/null +++ b/spatialLIBD/151675/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151675/processed_151675.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 300 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false diff --git a/spatialLIBD/151676/default.yaml b/spatialLIBD/151676/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f3a7c04890d87eb82de053f3d3e825190342a36b --- /dev/null +++ b/spatialLIBD/151676/default.yaml @@ -0,0 +1,110 @@ +seed: 42 + +data: + train_dir: "./sami/spatialLIBD/151676/processed_151676.h5ad" + val_dir: "" + infer_dir: "./data/infer" + file_pattern: "*.h5ad" + omics1_obsm_key: "expression_scaled_pca" + omics2_obsm_key: "path_feat" + omics1_target_obsm_key: "expression_scaled_pca" + omics2_target_obsm_key: "path_feat" + batch_size: 1 + num_workers: 0 + pin_memory: false + +model: + branch_mode: "multimodal_fusion" # Options: "omics1", "omics2", "multimodal_fusion" + hidden_dim: 64 + omics1_in_dim: 50 + omics2_in_dim: 1024 + omics1_target_dim: 50 + omics2_target_dim: 1024 + + omics1_encoder: + feature_adapter: + adapter_type: "mlp_bottleneck" + adapter_dim: 64 + dropout: 0.1 + force_linear: false + + omics1_augmentation: + enabled: false + alpha: 0.5 + + omics2_encoder: + adapter_type: "mlp_bottleneck" + adapter_dim: 512 + dropout: 0.1 + force_linear: false + + graph: + top_k: 6 + symmetrize: true + add_self_loops: false + chunk_size: 512 + + graph_backbone: + omics1: + type: "pointnext" + use_layer_transformer: true + omics2: + type: "pointnext" + use_layer_transformer: true + pointnext: + expansion: 4 + dropout: 0.1 + max_neighbors: null + pooling: "mean" + + cross_modal_attention: + num_heads: 4 + dropout: 0.1 + + gat: + num_layers: 3 + omics1_num_layers: 3 + omics2_num_layers: 3 + num_heads: 4 + dropout: 0.1 + leaky_relu_negative_slope: 0.2 + + layer_transformer: + num_heads: 4 + ff_dim: 256 + dropout: 0.1 + pooling: "mean" + + fusion: + mlp_hidden_dim: 256 + dropout: 0.1 + +train: + device: "cuda" + epochs: 400 + lr: 1.0e-3 + weight_decay: 1.0e-4 + grad_clip_norm: 5.0 + amp: false + log_interval: 10 + output_dir: "./outputs" + save_every: 20 + +loss: + lambda_omics1: 10.0 + lambda_omics2: 0.1 + lambda_contrastive: 0.5 + lambda_consistency: 1.0 + + contrastive: + use_symmetric_loss: false + + consistency: + temperature: 0.1 + projector_hidden_dim: 128 + projector_out_dim: 64 + +infer: + checkpoint_path: "" + output_path: "./outputs/infer_embeddings.pt" + save_reconstruction: false