初始化项目，由ModelHub XC社区提供模型

Model: kojima-lab/molcrawl-protein-sequence-gpt2-small
Source: Original Platform

.gitattributes

@@ -0,0 +1,35 @@
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.arrow filter=lfs diff=lfs merge=lfs -text
+*.bin filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
+*.ftz filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.joblib filter=lfs diff=lfs merge=lfs -text
+*.lfs.* filter=lfs diff=lfs merge=lfs -text
+*.mlmodel filter=lfs diff=lfs merge=lfs -text
+*.model filter=lfs diff=lfs merge=lfs -text
+*.msgpack filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.onnx filter=lfs diff=lfs merge=lfs -text
+*.ot filter=lfs diff=lfs merge=lfs -text
+*.parquet filter=lfs diff=lfs merge=lfs -text
+*.pb filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
+*.pt filter=lfs diff=lfs merge=lfs -text
+*.pth filter=lfs diff=lfs merge=lfs -text
+*.rar filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+saved_model/**/* filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.tar filter=lfs diff=lfs merge=lfs -text
+*.tflite filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.wasm filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text
+*tfevents* filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,67 @@
+---
+license: apache-2.0
+tags:
+- pytorch
+- gpt2
+- protein
+pipeline_tag: text-generation
+---
+
+# molcrawl-protein-sequence-gpt2-small
+
+## Model Description
+
+GPT-2 small (124M parameters) foundation model pre-trained on protein amino acid sequences from the MolCrawl dataset.
+
+- **Model Type**: gpt2
+- **Data Type**: Protein
+- **Training Date**: 2026-04-24
+
+## Usage
+
+```python
+from transformers import AutoModelForCausalLM, AutoTokenizer
+import torch
+
+model = AutoModelForCausalLM.from_pretrained("kojima-lab/molcrawl-protein-sequence-gpt2-small")
+tokenizer = AutoTokenizer.from_pretrained("kojima-lab/molcrawl-protein-sequence-gpt2-small")
+
+# Generate protein sequence
+prompt = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGT"
+inputs = tokenizer(prompt, return_tensors="pt")
+with torch.no_grad():
+    output_ids = model.generate(
+        **inputs,
+        max_new_tokens=50,
+        do_sample=True,
+        temperature=0.8,
+        eos_token_id=None,  # HF config.json has legacy eos_token_id=0; disable early stop
+        pad_token_id=0,
+    )
+print(tokenizer.decode(output_ids[0], skip_special_tokens=True))
+
+```
+
+## Source Code
+
+Training pipeline, configuration files, and data preparation scripts are
+available in the MolCrawl GitHub repository:
+[https://github.com/mmai-framework-lab/MolCrawl](https://github.com/mmai-framework-lab/MolCrawl)
+
+## License
+
+This model is released under the APACHE-2.0 license.
+
+## Citation
+
+If you use this model, please cite:
+
+```bibtex
+@misc{molcrawl_protein_sequence_gpt2_small,
+  title={molcrawl-protein-sequence-gpt2-small},
+  author={{RIKEN}},
+  year={2026},
+  publisher={{Hugging Face}},
+  url={{https://huggingface.co/kojima-lab/molcrawl-protein-sequence-gpt2-small}}
+}
+```

config.json

@@ -0,0 +1,35 @@
+{
+  "architectures": [
+    "GPT2LMHeadModel"
+  ],
+  "model_type": "gpt2",
+  "vocab_size": 33,
+  "n_positions": 1024,
+  "n_ctx": 1024,
+  "n_embd": 768,
+  "n_layer": 12,
+  "n_head": 12,
+  "n_inner": 3072,
+  "activation_function": "gelu_new",
+  "resid_pdrop": 0.1,
+  "embd_pdrop": 0.1,
+  "attn_pdrop": 0.1,
+  "layer_norm_epsilon": 1e-05,
+  "initializer_range": 0.02,
+  "use_cache": true,
+  "bos_token_id": 0,
+  "eos_token_id": 2,
+  "transformers_version": "4.0.0",
+  "_name_or_path": "riken-gpt2",
+  "_riken_model_args": {
+    "n_layer": 12,
+    "n_head": 12,
+    "n_embd": 768,
+    "block_size": 1024,
+    "bias": false,
+    "vocab_size": 33,
+    "dropout": 0.1
+  },
+  "_riken_bias": false,
+  "pad_token_id": 1
+}

model.safetensors

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:93a8d4a89ed2220f3b0b668a6d0afad271b132343954fcfdeb80850d979200f0
+size 343486080

pytorch_model.bin

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a713335969d98276789fc511695deca307f4fb26387e861bb3dca68a896ec3f5
+size 343087848

special_tokens_map.json

@@ -0,0 +1,10 @@
+{
+  "additional_special_tokens": [
+    "|"
+  ],
+  "cls_token": "<cls>",
+  "eos_token": "<eos>",
+  "mask_token": "<mask>",
+  "pad_token": "<pad>",
+  "unk_token": "<unk>"
+}

tokenizer.json

@@ -0,0 +1,167 @@
+{
+  "version": "1.0",
+  "truncation": null,
+  "padding": null,
+  "added_tokens": [
+    {
+      "id": 0,
+      "content": "<cls>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 1,
+      "content": "<pad>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 2,
+      "content": "<eos>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 3,
+      "content": "<unk>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 31,
+      "content": "|",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    },
+    {
+      "id": 32,
+      "content": "<mask>",
+      "single_word": false,
+      "lstrip": false,
+      "rstrip": false,
+      "normalized": false,
+      "special": true
+    }
+  ],
+  "normalizer": null,
+  "pre_tokenizer": null,
+  "post_processor": {
+    "type": "TemplateProcessing",
+    "single": [
+      {
+        "SpecialToken": {
+          "id": "<cls>",
+          "type_id": 0
+        }
+      },
+      {
+        "Sequence": {
+          "id": "A",
+          "type_id": 0
+        }
+      },
+      {
+        "SpecialToken": {
+          "id": "<eos>",
+          "type_id": 0
+        }
+      }
+    ],
+    "pair": [
+      {
+        "Sequence": {
+          "id": "A",
+          "type_id": 0
+        }
+      },
+      {
+        "Sequence": {
+          "id": "B",
+          "type_id": 1
+        }
+      }
+    ],
+    "special_tokens": {
+      "<cls>": {
+        "id": "<cls>",
+        "ids": [
+          0
+        ],
+        "tokens": [
+          "<cls>"
+        ]
+      },
+      "<eos>": {
+        "id": "<eos>",
+        "ids": [
+          2
+        ],
+        "tokens": [
+          "<eos>"
+        ]
+      }
+    }
+  },
+  "decoder": null,
+  "model": {
+    "type": "BPE",
+    "dropout": null,
+    "unk_token": "<unk>",
+    "continuing_subword_prefix": null,
+    "end_of_word_suffix": null,
+    "fuse_unk": false,
+    "byte_fallback": false,
+    "ignore_merges": false,
+    "vocab": {
+      "<cls>": 0,
+      "<pad>": 1,
+      "<eos>": 2,
+      "<unk>": 3,
+      "L": 4,
+      "A": 5,
+      "G": 6,
+      "V": 7,
+      "S": 8,
+      "E": 9,
+      "R": 10,
+      "T": 11,
+      "I": 12,
+      "D": 13,
+      "P": 14,
+      "K": 15,
+      "Q": 16,
+      "N": 17,
+      "F": 18,
+      "Y": 19,
+      "M": 20,
+      "H": 21,
+      "W": 22,
+      "C": 23,
+      "X": 24,
+      "B": 25,
+      "U": 26,
+      "Z": 27,
+      "O": 28,
+      ".": 29,
+      "-": 30,
+      "|": 31,
+      "<mask>": 32
+    },
+    "merges": []
+  }
+}

tokenizer_config.json

@@ -0,0 +1,64 @@
+{
+  "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
+    },
+    "31": {
+      "content": "|",
+      "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": [
+    "|"
+  ],
+  "bos_token": "<cls>",
+  "clean_up_tokenization_spaces": false,
+  "cls_token": "<cls>",
+  "eos_token": "<eos>",
+  "mask_token": "<mask>",
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "<pad>",
+  "tokenizer_class": "PreTrainedTokenizerFast",
+  "unk_token": "<unk>"
+}

training_args.json

@@ -0,0 +1,17 @@
+{
+  "iteration": 5000,
+  "best_val_loss": 2.814284086227417,
+  "early_stopping_counter": 4,
+  "learning_rate": 0.0006,
+  "batch_size": 12,
+  "block_size": 1024,
+  "model_args": {
+    "n_layer": 12,
+    "n_head": 12,
+    "n_embd": 768,
+    "block_size": 1024,
+    "bias": false,
+    "vocab_size": 33,
+    "dropout": 0.1
+  }
+}