Upload 10 files

config (3).json

@@ -0,0 +1,38 @@
+{
+  "_name_or_path": "facebook/esm2_t6_8M_UR50D",
+  "architectures": [
+    "EsmForTokenClassification"
+  ],
+  "attention_probs_dropout_prob": 0.0,
+  "classifier_dropout": null,
+  "emb_layer_norm_before": false,
+  "esmfold_config": null,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.0,
+  "hidden_size": 320,
+  "id2label": {
+    "0": "No binding site",
+    "1": "Binding site"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 1280,
+  "is_folding_model": false,
+  "label2id": {
+    "Binding site": 1,
+    "No binding site": 0
+  },
+  "layer_norm_eps": 1e-05,
+  "mask_token_id": 32,
+  "max_position_embeddings": 1026,
+  "model_type": "esm",
+  "num_attention_heads": 20,
+  "num_hidden_layers": 6,
+  "pad_token_id": 1,
+  "position_embedding_type": "rotary",
+  "token_dropout": true,
+  "torch_dtype": "float32",
+  "transformers_version": "4.32.1",
+  "use_cache": true,
+  "vocab_list": null,
+  "vocab_size": 33
+}

optimizer.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b87c1b79565801752e44cc7aed098e04f1260524419c5b891badba0ddd798c25
+size 59361093

pytorch_model (3).bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:533fc0f41a4509d035112616b31db134f51387ff2b1895fed14ee17058a3305f
+size 30989061

rng_state.pth

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6dd3a816ab8628e6038ecf426e93a907752049203fbc39b63fcde557182a866f
+size 14575

scheduler.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:068a9051a45626c38f7190ab6a85a94edf90ab8712919a65a71afff348cc9384
+size 627

special_tokens_map (3).json

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

tokenizer_config (3).json

@@ -0,0 +1,5 @@
+{
+  "clean_up_tokenization_spaces": true,
+  "model_max_length": 1024,
+  "tokenizer_class": "EsmTokenizer"
+}

trainer_state.json

@@ -0,0 +1,217 @@
+{
+  "best_metric": 0.6282620163217179,
+  "best_model_checkpoint": "esm2_t6_8M-binding-site-classification_2023-09-05_16-25-08/checkpoint-5598",
+  "epoch": 3.0,
+  "eval_steps": 500,
+  "global_step": 5598,
+  "is_hyper_param_search": false,
+  "is_local_process_zero": true,
+  "is_world_process_zero": true,
+  "log_history": [
+    {
+      "epoch": 0.11,
+      "learning_rate": 0.0005695234606678405,
+      "loss": 0.4679,
+      "step": 200
+    },
+    {
+      "epoch": 0.21,
+      "learning_rate": 0.0005676006526247637,
+      "loss": 0.3559,
+      "step": 400
+    },
+    {
+      "epoch": 0.32,
+      "learning_rate": 0.0005643970338296423,
+      "loss": 0.3089,
+      "step": 600
+    },
+    {
+      "epoch": 0.43,
+      "learning_rate": 0.0005599271278444283,
+      "loss": 0.2692,
+      "step": 800
+    },
+    {
+      "epoch": 0.54,
+      "learning_rate": 0.0005542111989267148,
+      "loss": 0.232,
+      "step": 1000
+    },
+    {
+      "epoch": 0.64,
+      "learning_rate": 0.0005472751601620024,
+      "loss": 0.2046,
+      "step": 1200
+    },
+    {
+      "epoch": 0.75,
+      "learning_rate": 0.00053915045598708,
+      "loss": 0.2237,
+      "step": 1400
+    },
+    {
+      "epoch": 0.86,
+      "learning_rate": 0.0005298739196371016,
+      "loss": 0.2119,
+      "step": 1600
+    },
+    {
+      "epoch": 0.96,
+      "learning_rate": 0.0005194876061626189,
+      "loss": 0.1905,
+      "step": 1800
+    },
+    {
+      "epoch": 1.0,
+      "eval_auc": 0.9261141394147127,
+      "eval_f1": 0.4530748302654477,
+      "eval_loss": 0.2022695094347,
+      "eval_precision": 0.30564833493171073,
+      "eval_recall": 0.8752367424242424,
+      "eval_runtime": 95.9675,
+      "eval_samples_per_second": 27.447,
+      "eval_steps_per_second": 3.439,
+      "step": 1866
+    },
+    {
+      "epoch": 1.07,
+      "learning_rate": 0.0005080386017735853,
+      "loss": 0.173,
+      "step": 2000
+    },
+    {
+      "epoch": 1.18,
+      "learning_rate": 0.0004955788103746674,
+      "loss": 0.1316,
+      "step": 2200
+    },
+    {
+      "epoch": 1.29,
+      "learning_rate": 0.00048223406367877986,
+      "loss": 0.1423,
+      "step": 2400
+    },
+    {
+      "epoch": 1.39,
+      "learning_rate": 0.00046793079280001864,
+      "loss": 0.1411,
+      "step": 2600
+    },
+    {
+      "epoch": 1.5,
+      "learning_rate": 0.00045279856311429995,
+      "loss": 0.1111,
+      "step": 2800
+    },
+    {
+      "epoch": 1.61,
+      "learning_rate": 0.00043690597637775135,
+      "loss": 0.1513,
+      "step": 3000
+    },
+    {
+      "epoch": 1.71,
+      "learning_rate": 0.00042032508141478175,
+      "loss": 0.1106,
+      "step": 3200
+    },
+    {
+      "epoch": 1.82,
+      "learning_rate": 0.0004031310474857221,
+      "loss": 0.1073,
+      "step": 3400
+    },
+    {
+      "epoch": 1.93,
+      "learning_rate": 0.0003854018235080123,
+      "loss": 0.1079,
+      "step": 3600
+    },
+    {
+      "epoch": 2.0,
+      "eval_auc": 0.9625828119645666,
+      "eval_f1": 0.39631155965817316,
+      "eval_loss": 0.10649576038122177,
+      "eval_precision": 0.24979947431420216,
+      "eval_recall": 0.9584753787878788,
+      "eval_runtime": 96.1903,
+      "eval_samples_per_second": 27.383,
+      "eval_steps_per_second": 3.431,
+      "step": 3732
+    },
+    {
+      "epoch": 2.04,
+      "learning_rate": 0.0003672177846758513,
+      "loss": 0.1161,
+      "step": 3800
+    },
+    {
+      "epoch": 2.14,
+      "learning_rate": 0.00034866136808035477,
+      "loss": 0.0703,
+      "step": 4000
+    },
+    {
+      "epoch": 2.25,
+      "learning_rate": 0.00032981669898213067,
+      "loss": 0.087,
+      "step": 4200
+    },
+    {
+      "epoch": 2.36,
+      "learning_rate": 0.000310769209430562,
+      "loss": 0.0662,
+      "step": 4400
+    },
+    {
+      "epoch": 2.47,
+      "learning_rate": 0.0002916052509587806,
+      "loss": 0.0602,
+      "step": 4600
+    },
+    {
+      "epoch": 2.57,
+      "learning_rate": 0.0002725076004735508,
+      "loss": 0.0788,
+      "step": 4800
+    },
+    {
+      "epoch": 2.68,
+      "learning_rate": 0.00025337097363328114,
+      "loss": 0.0511,
+      "step": 5000
+    },
+    {
+      "epoch": 2.79,
+      "learning_rate": 0.00023437809198903362,
+      "loss": 0.0506,
+      "step": 5200
+    },
+    {
+      "epoch": 2.89,
+      "learning_rate": 0.00021561505950973994,
+      "loss": 0.0554,
+      "step": 5400
+    },
+    {
+      "epoch": 3.0,
+      "eval_auc": 0.9730075655719146,
+      "eval_f1": 0.6282620163217179,
+      "eval_loss": 0.08585791289806366,
+      "eval_precision": 0.4672312733650252,
+      "eval_recall": 0.9586647727272727,
+      "eval_runtime": 96.1068,
+      "eval_samples_per_second": 27.407,
+      "eval_steps_per_second": 3.434,
+      "step": 5598
+    }
+  ],
+  "logging_steps": 200,
+  "max_steps": 9330,
+  "num_train_epochs": 5,
+  "save_steps": 500,
+  "total_flos": 1987518770082000.0,
+  "trial_name": null,
+  "trial_params": null
+}

training_args.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:00e62d9bc654e9fc3dddd9e18034c546c97f9692dc1da6a2867d54883b2c5c7c
+size 4091

vocab (3).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>