config/experiment/train_plddt.yaml

# @package _global_

# All parameters below will be merged with parameters from default configurations set above 
# this allows you to overwrite only specified parameters

# Options for training:
# - /data: [pdb, pdb_sp, pdb_sp_afesm, pdb_sp_afesme]
# - /model/architecture: 
#         [foldingdit_100M, foldingdit_360M, foldingdit_700M, 
#          foldingdit_1.1B, foldingdit_1.6B, foldingdit_3B]
# - /trainer: [default, fsdp]

defaults:
  - override /data: pdb
  - override /model: simplefold
  - override /model/architecture: foldingdit_100M
  - override /model/sampler: euler_maruyama
  - override /model/processor: protein_processor
  - override /callbacks: default
  - override /trainer: default
  - override /logger: tensorboard

# load_ckpt_path: [PATH_TO_YOUR_CKPT] # uncomment to load a checkpoint
seed: 12345

trainer:
  max_steps: 10000
  val_check_interval: 1000 # this controls BOTH checkpoint steps and validation
  accumulate_grad_batches: 1 # gradient accumulation

data:
  batch_size: 8 # should be the same as the number of GPUs
  num_workers: 16

model:
  _target_: models.simplefold.simplefold.SimpleFold
  ema_decay: 0.999
  clip_grad_norm_val: 2.0
  esm_model: "esm2_3B"
  plddt_training: True

  plddt_module:
    _target_: models.simplefold.torch.confidence_module.ConfidenceModule
    hidden_size: ${model.architecture.hidden_size}
    num_plddt_bins: 50
    transformer_blocks: 
      _target_: models.simplefold.torch.blocks.HomogenTrunk
      depth: 4
      block:
        _target_: models.simplefold.torch.blocks.TransformerBlock
        _partial_: true
        hidden_size: ${model.architecture.hidden_size}
        mlp_ratio: 4.0
        use_swiglu: True # SwiGLU FFN
        self_attention_layer:
          _target_: models.simplefold.torch.layers.EfficientSelfAttentionLayer
          _partial_: True
          hidden_size: ${model.architecture.hidden_size}
          num_heads: ${model.architecture.num_heads}
          qk_norm: True
          pos_embedder:
            _target_: models.simplefold.torch.pos_embed.AxialRotaryPositionEncoding
            in_dim: 4
            embed_dim: ${model.architecture.hidden_size}
            num_heads: ${model.architecture.num_heads}
            base: 100.0

  scheduler:
    _target_: onescience.utils.simplefold.lr_scheduler.LinearWarmup
    _partial_: true
    min_lr: 1e-6
    max_lr: ${model.optimizer.lr}
    warmup_steps: 5000

  architecture:
    esm_model: ${model.esm_model}

  sampler:
    num_timesteps: 150
    tau: 0.3

  processor:
    scale: 16.0
    ref_scale: 5.0
    multiplicity: 16 # number of copies per GPU