| { |
| "input_dim": 11, |
| "hidden_dims": [ |
| 50, |
| 50 |
| ], |
| "dropout": 0.3, |
| "learning_rate": 0.0001, |
| "weight_decay": 0.001, |
| "max_epochs": 1000, |
| "batch_size": 1024, |
| "n_iter_no_change": 10, |
| "tol": 0.0001, |
| "seed": 42, |
| "val_early_stopping_max_psms": null, |
| "val_subsample_seed": null, |
| "feature_columns": [ |
| "ion_matches", |
| "ion_match_intensity", |
| "irt_error", |
| "margin", |
| "median_margin", |
| "entropy", |
| "z-score", |
| "min_token_probability", |
| "std_token_probability", |
| "mass_error_da" |
| ], |
| "feature_names": [ |
| "Fragment Match Features", |
| "iRT Feature", |
| "Beam Features", |
| "Token Score Features", |
| "Mass Error (Da)" |
| ], |
| "features": { |
| "Fragment Match Features": { |
| "_target_": "winnow.calibration.features.fragment_match.FragmentMatchFeatures", |
| "mz_tolerance_ppm": 20, |
| "mz_tolerance_da": null, |
| "learn_from_missing": false, |
| "intensity_model_name": "Prosit_2025_intensity_22PTM", |
| "max_precursor_charge": 6, |
| "max_peptide_length": 30, |
| "unsupported_residues": [ |
| "[UNIMOD:5]", |
| "[UNIMOD:385]", |
| "(+25.98)" |
| ], |
| "model_input_constants": null, |
| "model_input_columns": { |
| "collision_energies": "collision_energy", |
| "fragmentation_types": "frag_type" |
| }, |
| "koina_server_url": "localhost:8500", |
| "koina_ssl": false, |
| "excluded_columns": [ |
| "complementary_ion_count", |
| "max_ion_gap", |
| "spectral_angle", |
| "xcorr" |
| ] |
| }, |
| "iRT Feature": { |
| "_target_": "winnow.calibration.features.retention_time.RetentionTimeFeature", |
| "train_fraction": 0.1, |
| "min_train_points": 5, |
| "learn_from_missing": false, |
| "seed": 42, |
| "irt_model_name": "Prosit_2025_irt_22PTM", |
| "max_peptide_length": 30, |
| "unsupported_residues": [ |
| "[UNIMOD:5]", |
| "[UNIMOD:385]", |
| "(+25.98)" |
| ], |
| "koina_server_url": "localhost:8500", |
| "koina_ssl": false |
| }, |
| "Beam Features": { |
| "_target_": "winnow.calibration.features.beam.BeamFeatures", |
| "excluded_columns": [ |
| "edit_distance" |
| ] |
| }, |
| "Token Score Features": { |
| "_target_": "winnow.calibration.features.token_score.TokenScoreFeatures" |
| }, |
| "Mass Error (Da)": { |
| "_target_": "winnow.calibration.features.mass_error.MassErrorDaFeature", |
| "residue_masses": { |
| "G": 57.021464, |
| "A": 71.037114, |
| "S": 87.032028, |
| "P": 97.052764, |
| "V": 99.068414, |
| "T": 101.04767, |
| "C": 103.009185, |
| "L": 113.084064, |
| "I": 113.084064, |
| "N": 114.042927, |
| "D": 115.026943, |
| "Q": 128.058578, |
| "K": 128.094963, |
| "E": 129.042593, |
| "M": 131.040485, |
| "H": 137.058912, |
| "F": 147.068414, |
| "R": 156.101111, |
| "Y": 163.063329, |
| "W": 186.079313, |
| "U": 150.953633, |
| "O": 237.147727, |
| "K[UNIMOD:1]": 170.105528, |
| "K[UNIMOD:3]": 354.172561, |
| "C[UNIMOD:4]": 160.030649, |
| "Q[UNIMOD:7]": 129.042594, |
| "R[UNIMOD:7]": 157.085127, |
| "N[UNIMOD:7]": 115.026943, |
| "S[UNIMOD:21]": 166.998359, |
| "T[UNIMOD:21]": 181.014009, |
| "Y[UNIMOD:21]": 243.02966, |
| "E[UNIMOD:27]": 111.032028, |
| "Q[UNIMOD:28]": 111.032029, |
| "K[UNIMOD:34]": 142.110613, |
| "R[UNIMOD:34]": 170.116761, |
| "M[UNIMOD:35]": 147.0354, |
| "P[UNIMOD:35]": 113.047679, |
| "K[UNIMOD:36]": 156.126263, |
| "R[UNIMOD:36]": 184.132411, |
| "K[UNIMOD:37]": 170.141913, |
| "N[UNIMOD:43]": 317.1223, |
| "K[UNIMOD:58]": 184.121178, |
| "K[UNIMOD:64]": 228.111007, |
| "K[UNIMOD:121]": 242.13789, |
| "K[UNIMOD:122]": 156.089878, |
| "N[UNIMOD:137]": 1330.46579, |
| "N[UNIMOD:148]": 682.254496, |
| "N[UNIMOD:159]": 1006.360143, |
| "R[UNIMOD:188]": 162.12124, |
| "K[UNIMOD:214]": 272.197026, |
| "K[UNIMOD:259]": 136.109162, |
| "R[UNIMOD:267]": 166.10938, |
| "Y[UNIMOD:275]": 192.053493, |
| "N[UNIMOD:305]": 1558.576797, |
| "N[UNIMOD:307]": 1720.62962, |
| "N[UNIMOD:308]": 1882.682444, |
| "N[UNIMOD:309]": 1412.518888, |
| "N[UNIMOD:310]": 1574.571711, |
| "N[UNIMOD:311]": 1736.624535, |
| "C[UNIMOD:312]": 222.013284, |
| "K[UNIMOD:481]": 132.12007, |
| "K[UNIMOD:737]": 357.257895, |
| "S[UNIMOD:737]": 316.19496, |
| "K[UNIMOD:747]": 214.095357, |
| "K[UNIMOD:1289]": 198.136828, |
| "K[UNIMOD:1363]": 196.121178, |
| "N[UNIMOD:1408]": 2318.815368, |
| "N[UNIMOD:1409]": 2027.719952, |
| "N[UNIMOD:1410]": 2173.77786, |
| "N[UNIMOD:1452]": 1168.412966, |
| "N[UNIMOD:1462]": 1476.523699, |
| "N[UNIMOD:1465]": 1492.518613, |
| "N[UNIMOD:1467]": 1517.550248, |
| "N[UNIMOD:1468]": 1533.545162, |
| "N[UNIMOD:1477]": 1638.576522, |
| "N[UNIMOD:1480]": 1654.571437, |
| "N[UNIMOD:1481]": 1663.608157, |
| "N[UNIMOD:1484]": 1679.603071, |
| "N[UNIMOD:1487]": 1695.597986, |
| "N[UNIMOD:1488]": 1703.614305, |
| "N[UNIMOD:1496]": 1777.651084, |
| "N[UNIMOD:1500]": 1800.629346, |
| "N[UNIMOD:1504]": 1816.62426, |
| "N[UNIMOD:1506]": 1824.640579, |
| "N[UNIMOD:1509]": 1841.655895, |
| "N[UNIMOD:1510]": 1849.672213, |
| "N[UNIMOD:1511]": 1850.692615, |
| "N[UNIMOD:1519]": 1923.708993, |
| "N[UNIMOD:1529]": 1970.698488, |
| "N[UNIMOD:1531]": 1978.677084, |
| "N[UNIMOD:1532]": 1980.730457, |
| "N[UNIMOD:1534]": 1986.693402, |
| "N[UNIMOD:1537]": 2003.708718, |
| "N[UNIMOD:1540]": 2021.757006, |
| "N[UNIMOD:1541]": 2028.740353, |
| "N[UNIMOD:1547]": 2044.735267, |
| "N[UNIMOD:1549]": 2060.730182, |
| "N[UNIMOD:1551]": 2068.746501, |
| "N[UNIMOD:1555]": 2085.761816, |
| "N[UNIMOD:1559]": 2101.756731, |
| "N[UNIMOD:1562]": 2110.793451, |
| "N[UNIMOD:1722]": 1647.613242, |
| "N[UNIMOD:1746]": 1907.714078, |
| "N[UNIMOD:1761]": 1152.418052, |
| "N[UNIMOD:1763]": 1209.439515, |
| "N[UNIMOD:1766]": 1314.470875, |
| "N[UNIMOD:1768]": 1355.497424, |
| "N[UNIMOD:1769]": 1371.492339, |
| "N[UNIMOD:1771]": 1501.555333, |
| "N[UNIMOD:1772]": 1615.598261, |
| "N[UNIMOD:1773]": 1662.587755, |
| "N[UNIMOD:1775]": 1761.656169, |
| "N[UNIMOD:1776]": 1818.677633, |
| "N[UNIMOD:1777]": 1865.667128, |
| "N[UNIMOD:1778]": 1866.687529, |
| "N[UNIMOD:1779]": 1898.677358, |
| "N[UNIMOD:1780]": 1939.703908, |
| "N[UNIMOD:1781]": 1964.735542, |
| "N[UNIMOD:1782]": 2011.725037, |
| "N[UNIMOD:1783]": 2012.745438, |
| "N[UNIMOD:1784]": 2052.751586, |
| "N[UNIMOD:1785]": 2069.766902, |
| "N[UNIMOD:1840]": 2206.788091, |
| "K[UNIMOD:1848]": 242.126657, |
| "K[UNIMOD:1849]": 214.131742, |
| "N[UNIMOD:1963]": 1962.682169, |
| "N[UNIMOD:1964]": 1994.709721, |
| "K[UNIMOD:2016]": 432.302109, |
| "N[UNIMOD:2028]": 2975.042981, |
| "N[UNIMOD:2029]": 2466.888927, |
| "[UNIMOD:1]": 42.010565, |
| "[UNIMOD:5]": 43.005814, |
| "[UNIMOD:214]": 144.102063, |
| "[UNIMOD:385]": -17.026549, |
| "[UNIMOD:737]": 229.162932, |
| "[UNIMOD:2016]": 304.207146, |
| "(+25.98)": 25.980265 |
| }, |
| "isotope_error_range": [ |
| 0, |
| 1 |
| ] |
| } |
| } |
| } |