yorzoi/train_config.json at main · Tom-Ellis-Lab/yorzoi · GitHub

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{
  "seed": 42,
  "batch_size": 30,
  "num_epochs": 250,
  "patience": 50,
  "finetune_epochs": 40,
  "randomize_track_order": true,
  "scheduler": "cosineannealingwr",
  "optimizer": {
    "method": "adamw",
    "weight_decay": 0.0000001,
    "lr": 0.00006
  },
  "path_to_samples": "/home/tds122/clex/data/samples_290625/samples_combined.pkl",
  "fwd_track_only": false,
  "subset_data": {
    "chr_loss": [
      "NC_001148.4",
      "NC_001147.6",
      "NC_001146.8",
      "NC_001145.3",
      "NC_001144.5",
      "NC_001143.9",
      "NC_001142.9",
      "NC_001140.6",
      "NC_001139.9",
      "NC_001138.5",
      "NC_001137.3",
      "NC_001141.2",
      "NC_001136.10",
      "NC_001135.5",
      "NC_001134.8",
      "NC_001133.9",
      "E145_NC_000007.14",
      "759h10_NC_000004.12",
      "802D1new_NC_000003.12",
      "852e11_NC_000009.12",
      "E533_NC_000007.14",
      "950c12_NC_000011.10",
      "E202_NC_000007.14",
      "E1068_NC_000007.14",
      "E481_NC_000007.14",
      "926e5_NC_000017.11"
    ]
  },
  "shuffle_train_loader": true,
  "shuffle_val_loader": false,
  "shuffle_test_loader": false,
  "plot_batch_train": false,
  "plot_batch_val": false,
  "loss": {
    "poisson_weight": 0.1,
    "epsilon": 0.00001,
    "reduction": "mean"
  },
  "borzoi_cfg": {
    "dim": 512,
    "resolution": 10,
    "depth": 8,
    "heads": 4,
    "return_center_bins_only": true,
    "attn_dim_key": 64,
    "attn_dim_value": 192,
    "dropout_rate": 0.2,
    "attn_dropout": 0.05,
    "pos_dropout": 0.01,
    "enable_mouse_head": false,
    "flashed": true,
    "horizontal_conv0": {
      "in_channels": 448,
      "out_channels": 324
    },
    "upsampling_unet0": {
      "in_channels": 324,
      "out_channels": 324
    },
    "separable1": {
      "conv1d": {
        "out_channels": 324
      },
      "separ_conv": {
        "in_channels": 512,
        "out_channels": 512
      }
    },
    "separable0": {
      "in_channels": 324,
      "out_channels": 324
    },
    "final_joined_convs": {
      "in_channels": 324,
      "out_channels": 162
    },
    "head": {
      "in_channels": 162,
      "out_channels": 162
    }
  },
  "augmentation": {
    "noise": false,
    "rc_aug": true
  }
}