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DNA-Embedding-Inversion

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DNA-Embedding-Inversion
File size: 5,063 Bytes
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data:
  shuffle: true
  mean: true
  multi: true
  require_sequence_disjoint: true
  source_schema: dna_inversion_hg38_multilen_v2
  source_corpus: data/hg38_multilen_seqdisjoint/hg38_multilen_seqdisjoint.h5
  ood_source_corpus: data/1000g_multilen_seqdisjoint/1000g_multilen_seqdisjoint.h5
  artifact_dir: data/hg38_multilen_seqdisjoint
  fm_slug: ntv2
  seq_lengths:
  - 10
  - 15
  - 20
  - 25
  - 30
  - 35
  - 40
  - 45
  - 50
  - 60
  - 70
  - 80
  - 90
  - 100
  train_seq_lengths:
  - 10
  - 15
  - 20
  - 25
  - 30
  - 35
  - 40
  - 45
  - 50
  - 60
  - 70
  - 80
  - 90
  - 100
  train_csvs:
  - ${data.artifact_dir}/train_${data.fm_slug}_10_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_15_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_20_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_25_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_30_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_35_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_40_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_45_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_50_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_60_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_70_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_80_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_90_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/train_${data.fm_slug}_100_hg38_multilen_seqdisjoint.h5
  val_csvs:
  - ${data.artifact_dir}/val_${data.fm_slug}_10_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_15_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_20_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_25_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_30_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_35_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_40_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_45_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_50_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_60_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_70_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_80_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_90_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/val_${data.fm_slug}_100_hg38_multilen_seqdisjoint.h5
  test_csvs:
  - ${data.artifact_dir}/test_${data.fm_slug}_10_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_15_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_20_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_25_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_30_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_35_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_40_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_45_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_50_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_60_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_70_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_80_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_90_hg38_multilen_seqdisjoint.h5
  - ${data.artifact_dir}/test_${data.fm_slug}_100_hg38_multilen_seqdisjoint.h5
  seq_length: 100
  skip_sha256_check: true
  normalization_method: standard
  subset_fraction: null
  embedding_dim: 1024
  tokenizer:
    type: huggingface
    model_name: InstaDeepAI/nucleotide-transformer-v2-500m-multi-species
  checkpoint: InstaDeepAI/nucleotide-transformer-v2-500m-multi-species
model:
  model_file_name: model/query_decoder.py
  model_name: query_decoder
  model_type: query_decoder
  mode: mean
  d_model: 384
  nhead: 8
  num_layers: 6
  dim_feedforward: 1536
  dropout: 0.1
  n_context_tokens: 16
  aux_length_loss_weight: 0.5
  output_dim: 4
  hidden_dims: []
optim:
  lr: 0.001
  weight_decay: 0.0001
  eps: 1.0e-06
  epochs: 20
  batch_size: 32
  num_workers: 16
  grad_clip_norm: 1.0
  use_scheduler: true
  scheduler:
    max_lr: 0.0005
    pct_start: 0.3
    anneal_strategy: cos
    div_factor: 25.0
    final_div_factor: 10000.0
train:
  seed: 42
  project: dna-embedding-inversion
  run_name: null
  use_wandb: false
  log_interval: 10000
  device: cuda:0
  early_stopping:
    enabled: false
    patience: 5
    min_delta: 1.0e-05
  max_val_samples: null
  nan_backoff:
    skip_frac_threshold: 0.02
    lr_backoff: 0.5