| exp_name: bag-base-lr3e-3-mse-ema999 | |
| data: | |
| patch_size: 4096 | |
| oversample: 2 | |
| val_oversample: 1 | |
| target_cells_per_subslide: 50000 | |
| target_partial_keep_ratio: 0.1 | |
| vocab: | |
| gene_vocab_size: 19228 | |
| organ_vocab_size: 12 | |
| platform_vocab_size: 4 | |
| gene_pad_id: 0 | |
| model: | |
| embed_dim: 384 | |
| encoder_depth: 8 | |
| encoder_heads: 6 | |
| predictor_depth: 3 | |
| predictor_heads: 3 | |
| predictor_dim: 192 | |
| mlp_ratio: 2.0 | |
| dropout: 0.1 | |
| gene_encoder: | |
| max_len: 512 | |
| spatial_encoding: | |
| normalize: center_scale | |
| alibi_scale: 1.0 | |
| masking: | |
| mask_ratio: 0.6 | |
| training: | |
| epochs: 100 | |
| total_steps: 10000 | |
| batch_size: 32 | |
| gradient_accumulation_steps: 1 | |
| learning_rate: 3e-3 | |
| weight_decay: 0.05 | |
| warmup_epochs: 10 | |
| warmup_steps: 1000 | |
| ema_start: 0.999 | |
| ema_end: 0.9999 | |
| num_workers: 2 | |
| grad_clip: 1.0 | |
| seed: 0 | |
| precision: bf16 | |
| logging: | |
| group: bag-scale | |
| output: | |
| save_every: 500 | |
| val_every: 50 | |