README.md

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license: cc-by-3.0 language: - en size_categories: - 1M<n<10M pretty_name: BIOSCAN-5M tags: - Multimodal_dataset - Large_dcale_dataset - Image - DNA_barcode - Taxonomy - Biodiversity - LLMs - BERT - Clustering - Multimodal_retrieval_learning - Zero_shot_transfer_learning - Geo_location - Specimen_size - Insect - Species maintainers: https://huggingface.co/Gharaee

Dataset Card for BIOSCAN-5M

Overview

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, we present the BIOSCAN-5M Insect dataset to the machine learning community. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, geographical information, and specimen size.

Citation

If you make use of the BIOSCAN-5M dataset and/or its code repository, please cite the following paper:

@inproceedings{gharaee2024bioscan5m,
    title={{BIOSCAN-5M}: A Multimodal Dataset for Insect Biodiversity},
    booktitle={Advances in Neural Information Processing Systems},
    author={Zahra Gharaee and Scott C. Lowe and ZeMing Gong and Pablo Millan Arias
        and Nicholas Pellegrino and Austin T. Wang and Joakim Bruslund Haurum
        and Iuliia Zarubiieva and Lila Kari and Dirk Steinke and Graham W. Taylor
        and Paul Fieguth and Angel X. Chang
    },
    editor={A. Globerson and L. Mackey and D. Belgrave and A. Fan and U. Paquet and J. Tomczak and C. Zhang},
    pages={36285--36313},
    publisher={Curran Associates, Inc.},
    year={2024},
    volume={37},
    url={https://proceedings.neurips.cc/paper_files/paper/2024/file/3fdbb472813041c9ecef04c20c2b1e5a-Paper-Datasets_and_Benchmarks_Track.pdf},
}

Dataset Features

Each configuration loads specimen images along with associated metadata fields:

• image
  RGB JPEG images of individual insect specimens.

• Metadata fields

  • Indexing fields
    • processid: A unique number assigned by BOLD (International Barcode of Life Consortium).
    • sampleid: A unique identifier given by the collector.
  • Taxonomic labels
    • phylum, class, order, family, subfamily, genus, species: Hierarchical taxonomic classification
  • Genetic information
    • dna_bin: Barcode Index Number
    • dna_barcode: DNA barcode sequence
  • Geographic data
    • country, province_state: Collection location
    • coord-lat, coord-lon: Latitude and longitude coordinates
  • Specimen size data
    • image_measurement_value: Measured image property (e.g., pixel area)
    • area_fraction: Fraction of the image occupied by the specimen
    • scale_factor: Relative size normalization factor
  • Split and localization
    • split: Data partition label (e.g., train, test, val)
    • chunk: Subdirectory label for scalable storage

Usage

To load the BIOSCAN-5M dataset from dataset.py

from datasets import load_dataset

ds = load_dataset("dataset.py", name="cropped_256_eval", split="validation", trust_remote_code=True)

ℹ️ Note: The CSV metadata and image package associated with the selected configuration will be automatically downloaded and extracted to ~/.cache/huggingface/datasets/downloads/extracted/ .

📑 Configurations

name	Available split values
cropped_256, original_256	pretrain, train, validation, test, val_unseen, test_unseen, key_unseen, other_heldout
cropped_256_pretrain, original_256_pretrain	pretrain
cropped_256_train, original_256_train	train
cropped_256_eval, original_256_eval	validation, test, val_unseen, test_unseen, key_unseen, other_heldout

ℹ️ Note: If you do not specify the split when loading the dataset, all available splits will be loaded as a dictionary.

Sample Usage

The usage_demo_bioscan5m.py script demonstrates how to load and visualize samples from the BIOSCAN-5M dataset.

To run the script, execute:

python usage_demo_bioscan5m.py

This will display 10 dataset samples, each showing the organism image on the right, and the corresponding metadata fields on the left, including taxonomic, geographic, genetic, and size-related information.

Dataset Access

To clone this dataset repository, use the following command:

GIT_LFS_SKIP_SMUDGE=1 git clone https://huggingface.co/datasets/bioscan-ml/BIOSCAN-5M

Dataset Sources

• Dataset website: https://biodiversitygenomics.net/5M-insects/
• GoogleDrive: https://drive.google.com/drive/u/1/folders/1Jc57eKkeiYrnUBc9WlIp-ZS_L1bVlT-0
• GitHub: https://github.com/zahrag/BIOSCAN-5M
• Zenodo: https://zenodo.org/records/11973457
• Kaggle: https://www.kaggle.com/datasets/zahragharaee/bioscan-5m/data
• Paper: https://arxiv.org/abs/2406.12723

Copyright and License

The images included in the BIOSCAN-5M dataset available through this repository are subject to copyright and licensing restrictions shown in the following:

• Copyright Holder: CBG Photography Group
• Copyright Institution: Centre for Biodiversity Genomics (email:CBGImaging@gmail.com)
• Photographer: CBG Robotic Imager
• Copyright License: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
• Copyright Contact: collectionsBIO@gmail.com
• Copyright Year: 2021