Add instanovo-phospho-v1.0.0 model

README.md

@@ -0,0 +1,10 @@
+---
+tags:
+- model_hub_mixin
+- pytorch_model_hub_mixin
+---
+
+This model has been pushed to the Hub using the [PytorchModelHubMixin](https://huggingface.co/docs/huggingface_hub/package_reference/mixins#huggingface_hub.PyTorchModelHubMixin) integration:
+- Code: [More Information Needed]
+- Paper: [More Information Needed]
+- Docs: [More Information Needed]

config.json

@@ -0,0 +1,115 @@
+{
+  "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"
+}

model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:59ac059b0a2b8b1c2b75c49ba35140984f897427baa5a43acb4c2feb24ef7fb2
+size 379105512