{
  "architecture": "FlipyFlopy",
  "ml": {
    "model": {
      "FlipyFlopy": {
        "embedsz": 256,
        "head": [
          16,
          16,
          64,
          "None",
          "None"
        ],
        "units": "None",
        "blocks": 9,
        "filtend": 512,
        "std": 0.01,
        "klw": 0.0001,
        "drop": 0.0
      }
    },
    "embedding": {
      "max_len": 40,
      "min_charge": 1,
      "max_charge": 8,
      "channel_first": true,
      "embedding_type": "EmbedPeptide",
      "embeddings": [
        "peptide",
        "mods",
        "charge",
        "nce_singleton"
      ],
      "nce_bins": [
        0,
        10,
        20,
        30,
        40,
        100
      ],
      "ev_range": [
        0,
        10,
        20,
        30,
        40,
        50,
        60,
        70,
        100
      ],
      "peptide": {
        "mods": [
          "Carbamidomethyl",
          "Oxidation",
          "Pyro-carbamidomethyl",
          "Glu->pyro-Glu",
          "Gln->pyro-Glu",
          "Methyl",
          "Phospho",
          "Acetyl",
          "iTRAQ4plex",
          "TMT6plex",
          "Deamidated"
        ]
      }
    },
    "batch_size": 100,
    "transfer_learning": false,
    "limit_train_batches": 1.0,
    "max_epochs": 60,
    "shuffle": true,
    "sampler": {
      "sampler_type": "LengthSampler",
      "max_length": 40,
      "min_length": 10,
      "scale": 1.0
    },
    "bayesian_network": {
      "bayes": false,
      "sample_nbr": 3
    },
    "loss": {
      "loss_function": "SpectrumCosineLoss",
      "sqrt_intensity": true
    },
    "metrics": [
      "SpectrumCosineMetric"
    ],
    "valid_metrics": null,
    "train_metrics": null,
    "optimizer": {
      "optimizer_function": "AdamW",
      "lr": 0.0003
    },
    "output_column": "spectrum",
    "precision": 32
  },
  "ms": {
    "bin_size": 0.1,
    "max_mz": 2000,
    "down_shift": 0.05,
    "dataloader": "TandemArrowDataset",
    "datamodule": "MasskitDataModule",
    "take_max": false,
    "take_sqrt": false,
    "columns": [
      "id",
      "charge",
      "peptide",
      "peptide_len",
      "nce",
      "ev",
      "mod_names",
      "mod_positions"
    ],
    "dataset_columns": [
      "id",
      "charge",
      "peptide",
      "peptide_len",
      "ev",
      "mod_names"
    ]
  }
}