README.md

---
license: cc-by-3.0
license_name: cc-by-3.0
license_link: https://creativecommons.org/licenses/by/3.0/
language:
  - en
tags:
  - ViT
  - ResNet
  - Transfer_learning
  - Fine_tuning
  - Classification
  - Vision
  - Taxonomy
  - Biodiversity
  - DNA_barcodes
  - Insects
  - Species
  - BigData
pretty_name: BIOSCAN-1M
size_categories:
  - 1M<n<10M
maintainers:
  - https://huggingface.co/Gharaee
author:
  name: Zahra Gharaee
  github: https://github.com/zahrag
  hf: https://huggingface.co/Gharaee
---

[![Author: zahrag](https://img.shields.io/badge/author-zahrag-blue)](https://huggingface.co/Gharaee)



# BIOSCAN-1M


<div align="center">
  <img src="images/Fig1.png" alt="Alt Text" width="1000" style="display: block; margin: 0 auto;">
</div>

### Overview

The BIOSCAN-1M dataset offers researchers detailed information about insects, with each record containing four primary attributes:

- DNA Barcode Sequence
- Barcode Index Number (BIN)
- Biological Taxonomy Classification
- RGB image



### Citation

If you make use of the BIOSCAN-1M dataset and/or its code repository, please cite the following paper:

```
cite as:

@inproceedings{gharaee2023step,
    title={A Step Towards Worldwide Biodiversity Assessment: The {BIOSCAN-1M} Insect Dataset},
    booktitle={Advances in Neural Information Processing Systems},
    author={Gharaee, Z. and Gong, Z. and Pellegrino, N. and Zarubiieva, I. and Haurum, J. B. and Lowe, S. C. and McKeown, J. T. A. and Ho, C. Y. and McLeod, J. and Wei, Y. C. and Agda, J. and Ratnasingham, S. and Steinke, D. and Chang, A. X. and Taylor, G. W. and Fieguth, P.},
    editor={A. Oh and T. Neumann and A. Globerson and K. Saenko and M. Hardt and S. Levine},
    pages={43593--43619},
    publisher={Curran Associates, Inc.},
    year={2023},
    volume={36},
    url={https://proceedings.neurips.cc/paper_files/paper/2023/file/87dbbdc3a685a97ad28489a1d57c45c1-Paper-Datasets_and_Benchmarks.pdf},
}
```

## Dataset Access

To clone this dataset repository, use the following command:

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

### 📦 Resources and Access

- **📄 Paper**: [arXiv](https://arxiv.org/abs/2307.10455)
- **🌐 Website**: [BIOSCAN-1M Project Page](https://biodiversitygenomics.net/1M_insects/)
- **💻 GitHub**: [bioscan-ml/BIOSCAN-1M](https://github.com/bioscan-ml/BIOSCAN-1M)
- **📁 Downloads**:
  - [Google Drive](https://drive.google.com/drive/u/1/folders/1kD9cXuQ1FdL30etp7sjy_Gs_NAAJ3EXI)
  - [Zenodo](https://zenodo.org/records/8030065)
  - [Kaggle](https://www.kaggle.com/datasets/zahragharaee/bioscan-1m-insect-dataset)


## BIOSCAN-1M Dataset Record

### I. DNA barcode sequence
The provided DNA barcode sequence showcases the arrangement of nucleotides:

* Adenine (A): Red 
* Thymine (T): Blue
* Cytosine (C): Green
* Guanine (G): Yellow
 
```
TTTATATTTTATTTTTGGAGCATGATCAGGAATAGTTGGAACTTCAATAAGTTTATTAATTCGAACAGAATTAAGCCAACCAGGAATTTTTA ...
```

<div align="center">
  <img src="images/DNA_sequence.png" alt="Alt Text" width="1000" style="display: block; margin: 0 auto;">
</div>


### II. Barcode Index Number (BIN)
BINs, acting as an alternative to Linnean names, provide a genetic-centric classification for organisms, 
emphasizing the significance of genetic code in taxonomy.

```
BOLD:AER5166
```

<div align="center">
  <img src="images/BIN.png" alt="Alt Text" width="1000" style="display: block; margin: 0 auto;">
</div>

### III. Biological taxonomy ranking annotations
Taxonomic group ranking annotations categorize organisms hierarchically based on evolutionary relationships.
It organizes species into groups based on shared characteristics and genetic relatedness.

<div align="center">
  <img src="images/Taxonomy_horiz_upd1.png" alt="Alt Text" width="1000" style="display: block; margin: 0 auto;">
</div>

  
### IV. RGB image
Original insect images from 16 most densly populated orders of the BIOSCAN-1M Insect dataset. 
The numbers below each image identify the number of images in each class, and clearly illustrate the degree of class imbalance in the BIOSCAN-1M Insect dataset.

<div align="center">
  <table>
    <!-- First Row -->
    <tr>
      <td align="center" ><img src="images/Diptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Hymenoptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Coleoptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Hemiptera.jpg" width="400px" height="400px" class="image"></td>
    </tr>
    <tr>
      <td align="center"><strong>Diptera: 896,234</strong></td>
      <td align="center"><strong>Hymenoptera: 89,311</strong></td> 
      <td align="center"><strong>Coleoptera: 47,328</strong></td>
      <td align="center"><strong>Hemiptera: 46,970</strong></td>
    </tr>
    <!-- Second Row -->
    <tr>
      <td align="center" ><img src="images/Lepidoptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Psocodea.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Thysanoptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Trichoptera.jpg" width="400px" height="400px" class="image"></td>
    </tr>
    <tr>
      <td align="center"><strong>Lepidoptera: 32,538</strong></td>
      <td align="center"><strong>Psocodea: 9,635</strong></td>
      <td align="center"><strong>Thysanoptera: 2,088</strong></td>
      <td align="center"><strong>Trichoptera: 1,296</strong></td>
    </tr>
    <!-- Third Row -->
    <tr>
      <td align="center" ><img src="images/Orthoptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Blattodea.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Neuroptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Ephemeroptera.jpg" width="400px" height="400px" class="image"></td>
    </tr>
    <tr>
      <td align="center"><strong>Orthoptera: 1,057</strong></td>
      <td align="center"><strong>Blattodea: 824</strong></td>
      <td align="center"><strong>Neuroptera: 676</strong></td>
      <td align="center"><strong>Ephemeroptera: 96</strong></td>
    </tr>
    <!-- Fourth Row -->
    <tr>
      <td align="center" ><img src="images/Dermaptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Archaeognatha.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Plecoptera.jpg" width="400px" height="400px" class="image"></td>
      <td align="center" ><img src="images/Embioptera.jpg" width="400px" height="400px" class="image"></td>
    </tr>
    <tr>
      <td align="center"><strong>Dermaptera: 66</strong></td>
      <td align="center"><strong>Archaeognatha: 63</strong></td>
      <td align="center"><strong>Plecoptera: 30</strong></td>
      <td align="center"><strong>Embioptera: 6</strong></td>
    </tr>
  </table>
</div>


## Class Distribution

Class distribution and class imbalance in the BIOSCAN-1M Insect dataset. Orders (top) and diptera families (bottom).
The image demonstrates that class imbalance is an inherent characteristic within the insect community.  


<div align="center">
  <img src="images/BIOSCAN_Fig2_upd3.png" alt="Alt Text" width="1000" style="display: block; margin: 0 auto;">
</div>