metadata
tags:
- biology
This dataset card contains data from the original Basenji project. The original Basenji dataset has two main limitations:
- Format: Data is stored in TensorFlow format, which is not directly compatible with PyTorch workflows
- Cost: Users need to pay Google Cloud storage fees to download the data
To facilitate PyTorch-based training, we have downloaded and converted the data to H5 format for our research usage (https://huggingface.co/papers/2506.01833). With permission from the original Basenji authors, we are releasing the H5-formatted data here for free access.
📁 Key Files
human_train.h5,human_valid.h5,human_test.h5mouse_train.h5,mouse_valid.h5,mouse_test.h5
📦 File Splitting & Reconstruction
Since the training files exceed 50GB and cannot be directly uploaded to 🤗 Hugging Face, we split them using the following commands:
split -b 45G -d -a 2 human_train.h5 human_train_part_
split -b 45G -d -a 2 mouse_train.h5 mouse_train_part_
After downloading all part files, you need to reconstruct the original H5 files:
# Reconstruct human_train.h5
cat human_train_part_* > human_train.h5
# Reconstruct mouse_train.h5
cat mouse_train_part_* > mouse_train.h5
📖 Citation
If you find this dataset useful, please cite both the original Basenji paper and our work:
@article{kelley2018sequential,
title={Sequential regulatory activity prediction across chromosomes with convolutional neural networks},
author={Kelley, David R and Reshef, Yakir A and Bileschi, Maxwell and Belanger, David and McLean, Cory Y and Snoek, Jasper},
journal={Genome research},
volume={28},
number={5},
pages={739--750},
year={2018},
publisher={Cold Spring Harbor Lab}
}
@inproceedings{yang2025space,
title={{SPACE}: Your Genomic Profile Predictor is a Powerful {DNA} Foundation Model},
author={Zhao Yang and Jiwei Zhu and Bing Su},
booktitle={Forty-second International Conference on Machine Learning},
year={2025},
url={https://openreview.net/forum?id=o4L9y4Jetm}
}