| seed: 42 | |
| data: | |
| mode: rna_he | |
| processed_h5: ./sami/Xenium_Human_Breast_Cancer_Rep1/processed_breast_cancer_rep1.h5 | |
| tile_manifest: ./sami/Xenium_Human_Breast_Cancer_Rep1/tiles/manifest.json | |
| num_workers: 0 | |
| pin_memory: false | |
| model: | |
| branch_mode: 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 | |
| omics2_encoder: | |
| adapter_type: mlp_bottleneck | |
| adapter_dim: 512 | |
| dropout: 0.1 | |
| force_linear: false | |
| omics1_augmentation: | |
| enabled: false | |
| alpha: 0.5 | |
| 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: 6 | |
| 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: 50 | |
| lr: 0.001 | |
| weight_decay: 0.0001 | |
| grad_clip_norm: 5.0 | |
| amp: false | |
| gradient_accumulation: 4 | |
| early_stopping_patience: 10 | |
| log_interval: 10 | |
| output_dir: ./outputs | |
| loss: | |
| lambda_omics1: 10.0 | |
| lambda_omics2: 10.0 | |
| 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 | |