commit 5a70c83150f55179eaf1c1ed1002de770d72779c Author: ModelHub XC Date: Wed Jun 3 00:46:20 2026 +0800 初始化项目，由ModelHub XC社区提供模型 Model: kojima-lab/molcrawl-genome-sequence-gpt2-small Source: Original Platform diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..a6344aa --- /dev/null +++ b/.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 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/dev/null +++ b/README.md @@ -0,0 +1,71 @@ +--- +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}} +} +``` diff --git a/added_tokens.json b/added_tokens.json new file mode 100644 index 0000000..0967ef4 --- /dev/null +++ b/added_tokens.json @@ -0,0 +1 @@ +{} diff --git a/config.json b/config.json new file mode 100644 index 0000000..6e7e7e8 --- /dev/null +++ b/config.json @@ -0,0 +1,44 @@ +{ + "_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, + 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"ATTCCCC": 3185, + "GTCATGC": 3186, + "GTTGGAA": 3187, + "TTAACCC": 3188, + "GGAGACC": 3189, + "TCCGGTC": 3190, + "TACACAC": 3191, + "ACCAGTT": 3192, + "GTTGCGAATCACTCTTAAAC": 3193, + "ATGTCGC": 3194, + "ACGCAGC": 3195, + "TGGCGG": 3196, + "TAGCATT": 3197, + "GCCGGCGC": 3198, + "TAAATG": 3199, + "GCCTTAA": 3200, + "GACCCTC": 3201, + "TATTTGC": 3202, + "GGATCAC": 3203, + "GTACCAC": 3204, + "GAACAGG": 3205, + "ATTCAGC": 3206, + "GCGCATT": 3207, + "AGTTGGTT": 3208, + "TAAACTCAAACACAACAACC": 3209, + "AACTCTT": 3210, + "ACCGCGGCTCATTGGGAC": 3211, + "GATCCCC": 3212, + "GCCATGG": 3213, + "ATCAAA": 3214, + "AACTTAA": 3215, + "GAACATT": 3216, + "GTGACCC": 3217, + "GATGGCTT": 3218, + "AGGAGAC": 3219, + "TTCGTAA": 3220, + "TTTTGAC": 3221, + "TACTGAA": 3222, + "GAAGCAC": 3223, + "ATCGGCC": 3224, + "AGGTTAC": 3225, + "TATCTAA": 3226, + "ATACAAAA": 3227, + "TTTTGGC": 3228, + "ATCAGAA": 3229, + "GGAACAA": 3230, + "GTCTGA": 3231, + "TGGTGTA": 3232, + "TATGATC": 3233, + "GTCTTCC": 3234, + 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+ "TATGGAA": 3336, + "ATCAAAGC": 3337, + "GTTGATA": 3338, + "ATTTGCC": 3339, + "AGGTGAC": 3340, + "GGAATAC": 3341, + "ACCTTAACAGGGCGTT": 3342, + "GGGAATC": 3343, + "GACGTGC": 3344, + "GAATGAC": 3345, + "TAATTGC": 3346, + "TACCTGC": 3347, + "ATTAGA": 3348, + "GGGTTAC": 3349, + "AGTGTTTT": 3350, + "AGGGTA": 3351, + "TGTACCC": 3352, + "TAAGCTT": 3353, + "ATTGGTC": 3354, + "TTCTCCCC": 3355, + "TCCTTGC": 3356, + "GGTACTC": 3357, + "TGAAAGCC": 3358, + "TCAACCAC": 3359, + "TAAGGTC": 3360, + "TGCGGTC": 3361, + "AGCACGC": 3362, + "TATTAAC": 3363, + "CGC": 3364, + "TGCCGGA": 3365, + "ATGACTC": 3366, + "TTTTGCC": 3367, + "TAGGATT": 3368, + "TTCATAC": 3369, + "CCCAGAA": 3370, + "GACAGAA": 3371, + "CAA": 3372, + "GATTACC": 3373, + "ATAAACC": 3374, + "GAGTCAC": 3375, + "GTTTCGC": 3376, + "GGCCGCGC": 3377, + "TGAGGAA": 3378, + "GACTTCC": 3379, + "GCCCTTC": 3380, + "GTGTCAC": 3381, + "GTTGTAC": 3382, + "GTCATCCC": 3383, + "TAACCAC": 3384, + "TAATCTT": 3385, + "GACAAGG": 3386, + "TACAAGC": 3387, + 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