Hugging Face's logo

InstaDeepAI
/
instanovo-phospho-v1.0.0

Text Generation
PyTorch
Safetensors
proteomics
mass-spectrometry
peptide-sequencing
de-novo-sequencing
phosphoproteomics
post-translational-modifications
transformer
biology
computational-biology
Model card Files
xet
Community
instanovo-phospho-v1.0.0
File size: 2,700 Bytes 
dd5fd45
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
 
{
  "LinearLR_end_factor": 0.05,
  "LinearLR_start_factor": 1.0,
  "LinearLR_total_iters": 300000,
  "STLR_cycle_length": 29591,
  "STLR_maxlr_list": [
    "2e-4",
    "1e-5",
    "5e-6",
    "5e-6",
    "5e-6",
    "5e-6",
    "2e-6",
    "2e-6",
    "2e-6",
    "2e-6"
  ],
  "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",
  "dim_feedforward": 1024,
  "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": [
    0,
    1
  ],
  "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": {
    "(ox)": "(+15.99)",
    "(p)": "(+79.97)"
  },
  "remove_precursor_tol": 2.0,
  "residues": {
    "A": 71.037114,
    "C": 103.009185,
    "C(+57.02)": 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(+15.99)": 147.0354,
    "N": 114.042927,
    "N(+.98)": 115.026943,
    "P": 97.052764,
    "Q": 128.058578,
    "Q(+.98)": 129.042594,
    "R": 156.101111,
    "S": 87.032028,
    "S(+79.97)": 166.998028,
    "T": 101.04767,
    "T(+79.97)": 181.01367,
    "V": 99.068414,
    "W": 186.079313,
    "Y": 163.063329,
    "Y(+79.97)": 243.029329
  },
  "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"
}