Upload 11 files

adapter_config.json

@@ -0,0 +1,29 @@
+{
+  "alpha_pattern": {},
+  "auto_mapping": null,
+  "base_model_name_or_path": "facebook/esm2_t12_35M_UR50D",
+  "bias": "none",
+  "fan_in_fan_out": false,
+  "inference_mode": true,
+  "init_lora_weights": true,
+  "layers_pattern": null,
+  "layers_to_transform": null,
+  "lora_alpha": 1,
+  "lora_dropout": 0.5,
+  "modules_to_save": null,
+  "peft_type": "LORA",
+  "r": 2,
+  "rank_pattern": {},
+  "revision": null,
+  "target_modules": [
+    "query",
+    "key",
+    "value",
+    "EsmSelfOutput.dense",
+    "EsmIntermediate.dense",
+    "EsmOutput.dense",
+    "EsmContactPredictionHead.regression",
+    "classifier"
+  ],
+  "task_type": "TOKEN_CLS"
+}

adapter_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c235fb9346636f37d8c19e324fa2b529176d36a6ff5174502c88a1561c5e6a9f
+size 316315

added_tokens.json

@@ -0,0 +1,7 @@
+{
+  "<cls>": 0,
+  "<eos>": 2,
+  "<mask>": 32,
+  "<pad>": 1,
+  "<unk>": 3
+}

optimizer.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b5aa2b398a4be37ced786504c18d8ec0cb59c0850bc911280cae3e090285f617
+size 613061

rng_state.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ce67784528ac7e58347bb8d23629b116d0ff23bac8b115f91f320db7044b5c80
+size 14575

scheduler.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0534d89b08eda6576e070ba72c3e1990acc80be84cb1aa614732f3f9d7c75b70
+size 627

special_tokens_map.json

@@ -0,0 +1,7 @@
+{
+  "cls_token": "<cls>",
+  "eos_token": "<eos>",
+  "mask_token": "<mask>",
+  "pad_token": "<pad>",
+  "unk_token": "<unk>"
+}

tokenizer_config.json

@@ -0,0 +1,54 @@
+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "<cls>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "<pad>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "<eos>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "3": {
+      "content": "<unk>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "32": {
+      "content": "<mask>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "additional_special_tokens": [],
+  "clean_up_tokenization_spaces": true,
+  "cls_token": "<cls>",
+  "eos_token": "<eos>",
+  "mask_token": "<mask>",
+  "model_max_length": 1024,
+  "pad_token": "<pad>",
+  "tokenizer_class": "EsmTokenizer",
+  "tokenizer_file": null,
+  "unk_token": "<unk>"
+}

trainer_state.json

@@ -0,0 +1,111 @@
+{
+  "best_metric": 0.2905413020689372,
+  "best_model_checkpoint": "esm2_t12_35M_qlora_binding_sites_2023-09-29_21-23-10/checkpoint-2620",
+  "epoch": 1.0,
+  "eval_steps": 500,
+  "global_step": 2620,
+  "is_hyper_param_search": false,
+  "is_local_process_zero": true,
+  "is_world_process_zero": true,
+  "log_history": [
+    {
+      "epoch": 0.08,
+      "learning_rate": 0.00036486016528034,
+      "loss": 0.438,
+      "step": 200
+    },
+    {
+      "epoch": 0.15,
+      "learning_rate": 0.0003492734066977151,
+      "loss": 0.2546,
+      "step": 400
+    },
+    {
+      "epoch": 0.23,
+      "learning_rate": 0.00032428866475798075,
+      "loss": 0.2093,
+      "step": 600
+    },
+    {
+      "epoch": 0.31,
+      "learning_rate": 0.00029133598412353574,
+      "loss": 0.1859,
+      "step": 800
+    },
+    {
+      "epoch": 0.38,
+      "learning_rate": 0.0002523014681276343,
+      "loss": 0.1708,
+      "step": 1000
+    },
+    {
+      "epoch": 0.46,
+      "learning_rate": 0.00020941932440723778,
+      "loss": 0.163,
+      "step": 1200
+    },
+    {
+      "epoch": 0.53,
+      "learning_rate": 0.0001651439861875321,
+      "loss": 0.1569,
+      "step": 1400
+    },
+    {
+      "epoch": 0.61,
+      "learning_rate": 0.00012200962857625793,
+      "loss": 0.1523,
+      "step": 1600
+    },
+    {
+      "epoch": 0.69,
+      "learning_rate": 8.248512069428916e-05,
+      "loss": 0.1496,
+      "step": 1800
+    },
+    {
+      "epoch": 0.76,
+      "learning_rate": 4.883271570665299e-05,
+      "loss": 0.1472,
+      "step": 2000
+    },
+    {
+      "epoch": 0.84,
+      "learning_rate": 2.2978566873028572e-05,
+      "loss": 0.1447,
+      "step": 2200
+    },
+    {
+      "epoch": 0.92,
+      "learning_rate": 6.402480854199967e-06,
+      "loss": 0.1448,
+      "step": 2400
+    },
+    {
+      "epoch": 0.99,
+      "learning_rate": 5.321843352333027e-08,
+      "loss": 0.1456,
+      "step": 2600
+    },
+    {
+      "epoch": 1.0,
+      "eval_accuracy": 0.9158318765632355,
+      "eval_auc": 0.8735825732790565,
+      "eval_f1": 0.2905413020689372,
+      "eval_loss": 0.3306124210357666,
+      "eval_mcc": 0.3586807785767391,
+      "eval_precision": 0.17611340104588588,
+      "eval_recall": 0.829501533305547,
+      "eval_runtime": 1771.8069,
+      "eval_samples_per_second": 124.517,
+      "eval_steps_per_second": 0.733,
+      "step": 2620
+    }
+  ],
+  "logging_steps": 200,
+  "max_steps": 2620,
+  "num_train_epochs": 1,
+  "save_steps": 500,
+  "total_flos": 1.7844788489074154e+17,
+  "trial_name": null,
+  "trial_params": null
+}

training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:70916536159e8f49c14bfc361f276beb2fe22b94043a7c3dd180844e4002c97c
+size 4155

vocab.txt

@@ -0,0 +1,33 @@
+<cls>
+<pad>
+<eos>
+<unk>
+L
+A
+G
+V
+S
+E
+R
+T
+I
+D
+P
+K
+Q
+N
+F
+Y
+M
+H
+W
+C
+X
+B
+U
+Z
+O
+.
+-
+<null_1>
+<mask>