config.json

{
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  "STLR_midpoint_fraction": 0.1,
  "STLR_ratio": 0.03125,
  "apply_lora": false,
  "console_logging_steps": 1000,
  "custom_encoder": null,
  "dec_precursor_sos": false,
  "dec_type": "instanovo",
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  "dim_intensity": null,
  "dim_model": 768,
  "dropout": 0.1,
  "enc_type": "instanovo",
  "epoch_transitions_only": true,
  "epochs": 10,
  "fine_tune": true,
  "grad_accumulation": 1,
  "gradient_clip_val": 10.0,
  "isotope_error_range": [
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  "learning_rate": "2e-4",
  "logger": null,
  "lora_rank": 64,
  "max_charge": 10,
  "max_length": 30,
  "max_mz": 2500.0,
  "min_delta": 0.002,
  "min_intensity": 0.01,
  "min_mz": 50.0,
  "model_save_folder_path": "./checkpoints/instanovo-ft/",
  "n_beams": 2,
  "n_gpu": 1,
  "n_head": 16,
  "n_layers": 9,
  "n_log": 1,
  "n_peaks": 200,
  "n_workers": 8,
  "num_sanity_val_steps": 10,
  "optimizer": "Adam",
  "patience": 1,
  "peak_dropout": 0.0,
  "precursor_mass_tol": 50,
  "predict_batch_size": 2220,
  "progress_bar": false,
  "ptms": {
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    "(p)": "(+79.97)"
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  "restore_best": true,
  "resume_checkpoint": "./checkpoints/extended_2e6da747/epoch=10-step=1000000.ckpt",
  "save_model": false,
  "save_weights_only": false,
  "schedule": "finetune_schedule_gu_encoder-decoder-v2.yaml",
  "scheduler": "STLRSchedulerEpochBased",
  "scheduler_interval": "step",
  "tb_summarywriter": "s3://dtu-denovo-s-2e6da747d6d34f62-outputs/logs/4e5ef73c-171c-41b0-8a3a-fff4ff97512c/",
  "tensorboard_logging_steps": 200,
  "train_batch_size": 64,
  "train_from_scratch": false,
  "train_num_shards": 0,
  "train_subset": 1.0,
  "use_depthcharge": false,
  "use_dvc": false,
  "val_check_interval": 7397,
  "valid_subset": 0.02,
  "weight_decay": "1e-6"
}