README.md

---
license: mit
license_name: cc-by-3.0
license_link: https://creativecommons.org/licenses/by/3.0/
language:
- en
tags:
- ViT
- Classification
- Vision
- Taxonomy
- Biodiversity
- DNA-Barcodes
- Insects
- Species
- BigData
---


# BIOSCAN_1M Insect Dataset


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



Website: https://biodiversitygenomics.net/1M_insects/

GitHub: https://github.com/zahrag/BIOSCAN-1M

Zenodo: https://zenodo.org/records/8030065

Kaggle: https://www.kaggle.com/datasets/zahragharaee/bioscan-1m-insect-dataset

Paper: https://arxiv.org/abs/2307.10455

```
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},
}
```



## A Dataset Record
BIOSCAN dataset provides researchers with information about insects. 
Each record of the BIOSCAN-1M Insect dataset contains four primary attributes:

* DNA barcode sequence
* Barcode Index Number (BIN)
* Biological taxonomy ranking annotations
* RGB image



###### <h4> 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 ...
```

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


###### <h4> 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
```

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

###### <h4> 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.

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

  
###### <h4> 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.  


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