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

.gitattributes

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README.md

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+---
+license: apache-2.0
+tags:
+- pytorch
+- gpt2
+- dna-genome
+pipeline_tag: text-generation
+---
+
+# molcrawl-genome-sequence-gpt2-small
+
+## Model Description
+
+GPT-2 small (124M parameters) foundation model pre-trained on human genome DNA sequences from the [GRCh38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/) reference assembly.
+
+## Datasets
+
+- **GRCh38 human genome reference assembly**: [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/) (Pre-training corpus)
+
+- **Model Type**: gpt2
+- **Data Type**: DNA/Genome
+- **Training Date**: 2026-04-24
+
+## Usage
+
+```python
+from transformers import AutoModelForCausalLM, AutoTokenizer
+import torch
+
+model = AutoModelForCausalLM.from_pretrained("kojima-lab/molcrawl-genome-sequence-gpt2-small")
+tokenizer = AutoTokenizer.from_pretrained("kojima-lab/molcrawl-genome-sequence-gpt2-small")
+
+# Generate DNA/genome sequence
+prompt = "ATCGATCGATCGATCGATCGATCGATCGATCG"
+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_genome_sequence_gpt2_small,
+  title={molcrawl-genome-sequence-gpt2-small},
+  author={{RIKEN}},
+  year={2026},
+  publisher={{Hugging Face}},
+  url={{https://huggingface.co/kojima-lab/molcrawl-genome-sequence-gpt2-small}}
+}
+```

added_tokens.json

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+{}

config.json

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+{
+  "_name_or_path": "learning_source_20260316/genome_sequence/gpt2-output/genome_sequence-small/checkpoint-200000",
+  "_riken_bias": false,
+  "_riken_model_args": {
+    "bias": false,
+    "block_size": 1024,
+    "dropout": 0.0,
+    "n_embd": 768,
+    "n_head": 12,
+    "n_layer": 12,
+    "vocab_size": 4096
+  },
+  "activation_function": "gelu_new",
+  "architectures": [
+    "GPT2LMHeadModel"
+  ],
+  "attn_pdrop": 0.0,
+  "bos_token_id": 1,
+  "embd_pdrop": 0.0,
+  "eos_token_id": 2,
+  "initializer_range": 0.02,
+  "layer_norm_epsilon": 1e-05,
+  "model_type": "gpt2",
+  "n_ctx": 1024,
+  "n_embd": 768,
+  "n_head": 12,
+  "n_inner": 3072,
+  "n_layer": 12,
+  "n_positions": 1024,
+  "reorder_and_upcast_attn": false,
+  "resid_pdrop": 0.0,
+  "scale_attn_by_inverse_layer_idx": false,
+  "scale_attn_weights": true,
+  "summary_activation": null,
+  "summary_first_dropout": 0.1,
+  "summary_proj_to_labels": true,
+  "summary_type": "cls_index",
+  "summary_use_proj": true,
+  "torch_dtype": "float32",
+  "transformers_version": "4.45.1",
+  "use_cache": true,
+  "vocab_size": 4096,
+  "pad_token_id": 0
+}

generation_config.json

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+{
+  "_from_model_config": true,
+  "bos_token_id": 0,
+  "eos_token_id": 0,
+  "transformers_version": "4.45.1"
+}

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special_tokens_map.json

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+  "bos_token": "<s>",
+  "eos_token": "</s>",
+  "unk_token": "<unk>"
+}

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tokenizer_config.json

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+{
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+      "lstrip": false,
+      "normalized": false,
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+      "single_word": false,
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+  "tokenizer_class": "PreTrainedTokenizerFast",
+  "unk_token": "<unk>"
+}

training_args.json

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+{
+  "iteration": 200000,
+  "best_val_loss": 5.296863555908203,
+  "early_stopping_counter": 17,
+  "learning_rate": 6e-06,
+  "batch_size": 12,
+  "block_size": 1024,
+  "model_args": {
+    "n_layer": 12,
+    "n_head": 12,
+    "n_embd": 768,
+    "block_size": 1024,
+    "bias": false,
+    "vocab_size": 4096,
+    "dropout": 0.0
+  }
+}