instanovo-v1.1.0 / config.json
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{
"blacklist": null,
"ckpt_interval": 100000,
"column_remapping": null,
"compile_model": true,
"console_logging_steps": 2000,
"conv_peak_encoder": false,
"dim_feedforward": 1024,
"dim_model": 768,
"dropout": 0.1,
"epochs": 30,
"fp16": true,
"grad_accumulation": 1,
"gradient_clip_val": 10.0,
"isotope_error_range": [
0,
1
],
"lazy_loading": true,
"learning_rate": 5e-05,
"logger": null,
"max_charge": 10,
"max_iters": 3000000,
"max_length": 40,
"max_mz": 2500.0,
"max_shard_size": 1000000,
"min_intensity": 0.01,
"min_mz": 50.0,
"model_save_folder_path": "checkpoints/instanovo-extended-massivekb",
"n_beams": 5,
"n_gpu": 1,
"n_head": 16,
"n_layers": 9,
"n_peaks": 200,
"num_sanity_val_steps": 10,
"perform_data_checks": true,
"precursor_mass_tol": 50,
"predict_batch_size": 64,
"preshuffle_shards": true,
"remove_precursor_tol": 2.0,
"report_to": "neptune",
"residue_remapping": null,
"residues": {
"A": 71.037114,
"C": 103.009185,
"C[UNIMOD:4]": 160.030649,
"D": 115.026943,
"E": 129.042593,
"F": 147.068414,
"G": 57.021464,
"H": 137.058912,
"I": 113.084064,
"K": 128.094963,
"L": 113.084064,
"M": 131.040485,
"M[UNIMOD:35]": 147.0354,
"N": 114.042927,
"N[UNIMOD:7]": 115.026943,
"P": 97.052764,
"Q": 128.058578,
"Q[UNIMOD:7]": 129.042594,
"R": 156.101111,
"S": 87.032028,
"S[UNIMOD:21]": 166.998028,
"T": 101.04767,
"T[UNIMOD:21]": 181.01367,
"V": 99.068414,
"W": 186.079313,
"Y": 163.063329,
"Y[UNIMOD:21]": 243.029329,
"[UNIMOD:1]": 42.010565,
"[UNIMOD:385]": -17.026549,
"[UNIMOD:5]": 43.005814
},
"resume_checkpoint": null,
"run_name": "instanovo_acpt_base",
"save_model": true,
"save_weights_only": false,
"seed": 101,
"tb_summarywriter": "s3://dtu-denovo-s-2e6da747d6d34f62-outputs/output/8cbd543a-56cb-4866-a257-731cc32e822b/tensorboard/",
"tensorboard_logging_steps": 500,
"train_batch_size": 128,
"train_from_scratch": true,
"train_partition": null,
"train_path": "/mnt/instanovo-data-kyber/identity_splits_parquet/*/*-train-*.parquet",
"train_subset": 1.0,
"use_flash_attention": false,
"use_shards": true,
"val_check_interval": 1.0,
"valid_partition": null,
"valid_path": "/mnt/instanovo-data-kyber/identity_splits_parquet/*/*-valid-*.parquet",
"valid_subset": 0.01,
"valid_subset_of_train": null,
"validate_precursor_mass": false,
"verbose_loading": true,
"warmup_iters": 100000,
"weight_decay": 1e-05
}