---
title: fungi-histone-modifications
canonical_url: "https://www.modelscope.cn/datasets/zhangtaolab/fungi-histone-modifications"
md_url: "https://www.modelscope.cn/datasets/zhangtaolab/fungi-histone-modifications.md"
repository: zhangtaolab/fungi-histone-modifications
last_updated: 2026-09-18
license: cc-by-nc-4.0
storage_size: "152 MB"
downloads: 284
stars: 0
---

# fungi-histone-modifications

> fungi-histone-modifications - zhangtaolab 在 ModelScope 开源的数据集。fungi-histone-modifications

zhangtaolab/fungi-histone-modifications 是 ModelScope 魔搭社区上的数据集，存储大小 152 MB，采用 cc-by-nc-4.0 许可。

- **Repository**: zhangtaolab/fungi-histone-modifications
- **License**: cc-by-nc-4.0
- **Storage size**: 152 MB
- **Downloads**: 284
- **Stars**: 0
- **Last updated**: 2026-09-18

Source: https://www.modelscope.cn/datasets/zhangtaolab/fungi-histone-modifications

---

# fungi-histone-modifications

**12 fungal histone-mark binary classification tasks** — each subset is a ready-to-use `train/dev/test.csv` (columns: `sequence,label`; 500 bp windows) for fine-tuning DNA foundation models.

## Subsets (12)

| Subset | Source | Description |
|---|---|---|
| `H3` | GUE EMP | Histone H3 bound regions (*S. cerevisiae* ChIP-chip) |
| `H3K4me1` | GUE EMP | H3K4 monomethylation |
| `H3K4me2` | GUE EMP | H3K4 dimethylation |
| `H3K4me3` | GUE EMP | H3K4 trimethylation (active promoters) |
| `H3K9ac` | GUE EMP | H3K9 acetylation |
| `H3K14ac` | GUE EMP | H3K14 acetylation |
| `H3K36me3` | GUE EMP | H3K36 trimethylation (gene bodies) |
| `H3K79me3` | GUE EMP | H3K79 trimethylation |
| `H4` | GUE EMP | Histone H4 bound regions |
| `H4ac` | GUE EMP | H4 acetylation |
| `H3K27ac` ★ | Fungal public data | H3K27 acetylation (active enhancers) |
| `H3K27me3` ★ | Fungal public data | H3K27 trimethylation (Polycomb repression) |

> ★ `H3K27ac` and `H3K27me3` were built from public fungal datasets; the remaining 10 subsets are sourced from the [GUE](https://github.com/lingxinzhou/GUE) benchmark.

## Usage

```bash
python scripts/huggingface/finetune.py \
    --pretrained_model models/FungiHelixSeek \
    --dataset_dir data/Bio_finetune_data/fungi-histone-modifications/H3K4me3 \
    --output_dir tmp/finetune_output \
    --tokens_length 512 --num_train_epochs 3
```

12 fine-tuned models (`FungiHelixSeek-H3` … `FungiHelixSeek-H3K27me3`) are released in the [FungiHelixSeek collection](https://huggingface.co/collections/zhangtaolab/fungihelixseek).

## License

CC-BY-NC 4.0 (research use; contact authors for commercial licensing).