Upload ESM2 protein model

README.md

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+# ESM2 Protein Model
+
+This is the protein component of a jointly trained NT-ESM2 model pair for DNA-protein analysis.
+
+## Model Details
+
+- **Model Type**: ESM2 for protein sequences
+- **Training**: Jointly trained with NT DNA model
+- **Architecture**: Transformer-based language model for proteins
+
+## Usage
+
+```python
+from transformers import AutoModel, AutoTokenizer
+
+# Load model and tokenizer
+model = AutoModel.from_pretrained("vsubasri/joint-nt-esm2-transcript-coding-protein")
+tokenizer = AutoTokenizer.from_pretrained("vsubasri/joint-nt-esm2-transcript-coding-protein")
+
+# Example usage
+protein_sequence = "MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGG"
+inputs = tokenizer(protein_sequence, return_tensors="pt")
+outputs = model(**inputs)
+```
+
+## Training Details
+
+- Jointly trained with DNA sequences for cross-modal understanding
+- Large model variant
+- Transcript-specific protein coding sequences
+
+## Files
+
+- `config.json`: Model configuration
+- `model.safetensors`: Model weights  
+- `tokenizer_config.json`: Tokenizer configuration
+- `vocab.txt`: Vocabulary file
+- `special_tokens_map.json`: Special tokens mapping
+
+## Citation
+
+If you use this model, please cite the original ESM2 paper and your joint training work.

config.json

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+{
+  "architectures": [
+    "EsmForMaskedLM"
+  ],
+  "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": 640,
+  "initializer_range": 0.02,
+  "intermediate_size": 2560,
+  "is_folding_model": false,
+  "layer_norm_eps": 1e-05,
+  "mask_token_id": 32,
+  "max_position_embeddings": 1026,
+  "model_type": "esm",
+  "num_attention_heads": 20,
+  "num_hidden_layers": 30,
+  "pad_token_id": 1,
+  "position_embedding_type": "rotary",
+  "token_dropout": true,
+  "torch_dtype": "float32",
+  "transformers_version": "4.51.3",
+  "use_cache": true,
+  "vocab_list": null,
+  "vocab_size": 33
+}

model.safetensors

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d9d799b9366ace791cc66e03b0c3b82dc4092bb37de1744b8472f41994b6639a
+size 595249400

special_tokens_map.json

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+{
+  "cls_token": "<cls>",
+  "eos_token": "<eos>",
+  "mask_token": "<mask>",
+  "pad_token": "<pad>",
+  "unk_token": "<unk>"
+}

tokenizer_config.json

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+{
+  "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
+    }
+  },
+  "clean_up_tokenization_spaces": false,
+  "cls_token": "<cls>",
+  "eos_token": "<eos>",
+  "extra_special_tokens": {},
+  "mask_token": "<mask>",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "<pad>",
+  "tokenizer_class": "EsmTokenizer",
+  "unk_token": "<unk>"
+}

vocab.txt

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+<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>