File size: 1,816 Bytes
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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
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