| { |
| "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" |
| ] |
| } |
| } |
