Add instanovo-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

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+{
+  "ckpt_interval": 100000,
+  "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
+  ],
+  "learning_rate": 5e-05,
+  "logger": null,
+  "max_charge": 10,
+  "max_iters": 3000000,
+  "max_length": 40,
+  "max_mz": 2500.0,
+  "min_intensity": 0.01,
+  "min_mz": 50.0,
+  "model_save_folder_path": "checkpoints/instanovo-extended",
+  "n_beams": 5,
+  "n_gpu": 1,
+  "n_head": 16,
+  "n_layers": 9,
+  "n_peaks": 200,
+  "n_workers": 16,
+  "num_sanity_val_steps": 10,
+  "precursor_mass_tol": 50,
+  "predict_batch_size": 64,
+  "remove_precursor_tol": 2.0,
+  "report_to": "neptune",
+  "residue_remapping": {
+    "M(ox)": "M(+15.99)",
+    "S(p)": "S(+79.97)",
+    "T(p)": "T(+79.97)",
+    "Y(p)": "Y(+79.97)"
+  },
+  "residues": {
+    "(+25.98)": 25.980265,
+    "(+42.01)": 42.010565,
+    "(+43.01)": 43.005814,
+    "(-17.03)": -17.026549,
+    "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
+  },
+  "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/logs/38aa4b76-2c51-4b4a-8d91-23c2a97f27bc/",
+  "tensorboard_logging_steps": 500,
+  "train_batch_size": 128,
+  "train_from_scratch": true,
+  "train_path": "data/extended",
+  "train_subset": 1.0,
+  "use_flash_attention": false,
+  "use_shards": true,
+  "val_check_interval": 1.0,
+  "valid_path": "data/extended",
+  "valid_subset": 0.01,
+  "valid_subset_of_train": null,
+  "warmup_iters": 100000,
+  "weight_decay": 1e-05
+}

model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:d3b8b2aa2ab7bdf2ef0f227e23638cd07e6800ac3c7e8719948fe028d6095a5d
+size 379130104