https://github.com/arindam369/medmnist-vit

Based on our paper "Implementing vision transformer for classifying 2D biomedical images" published in Scientific Reports (Nature)
https://github.com/arindam369/medmnist-vit

biomedical-image-classification bloodmnist breastmnist deep-learning medmnistv2 pathmnist retinamnist vision-transformer

Last synced: about 6 hours ago
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Based on our paper "Implementing vision transformer for classifying 2D biomedical images" published in Scientific Reports (Nature)

• Host: GitHub
• URL: https://github.com/arindam369/medmnist-vit
• Owner: arindam369
• License: mit
• Created: 2023-12-29T20:14:08.000Z (11 months ago)
• Default Branch: main
• Last Pushed: 2024-06-02T06:42:32.000Z (6 months ago)
• Last Synced: 2024-06-02T14:28:38.154Z (6 months ago)
• Topics: biomedical-image-classification, bloodmnist, breastmnist, deep-learning, medmnistv2, pathmnist, retinamnist, vision-transformer
• Language: Jupyter Notebook
• Homepage: https://doi.org/10.1038/s41598-024-63094-9
• Size: 3.72 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
[![DOI](https://zenodo.org/badge/DOI/10.1038/s41598-024-63094-9.svg)](https://doi.org/10.1038/s41598-024-63094-9)

# Implementing Vision Transformer for Classifying 2D Biomedical Images

Arindam Halder, Sanghita Gharami, Priyangshu Sadhu, Pawan Kumar Singh[[0000-0002-9598-7981](https://orcid.org/0000-0002-9598-7981)], Marcin Wozniak*[[0000-0002-9073-5347](https://orcid.org/0000-0002-9073-5347)], Muhammad Fazal Ijaz*[[0000-0001-5206-272X](https://orcid.org/0000-0001-5206-272X)]

(* Corresponding Authors)

This is the official implementation of the paper, "[Implementing vision transformer for classifying 2D biomedical images](https://www.nature.com/articles/s41598-024-63094-9)" published in "Scientific Reports (Nature)"

## Directory Structure

```

+-- gradcam

|   +-- .

|   +-- GradCam_BloodMNIST.ipynb

|   +-- GradCam_BreastMNIST.ipynb

|   +-- GradCam_PathMNIST.ipynb

|   +-- GradCam_RetinaMNIST.ipynb

+-- images

+-- BloodMNIST.ipynb

+-- BreastMNIST.ipynb

+-- PathMNIST.ipynb

+-- RetinaMNIST.ipynb

```

**Note:** ``images`` folder contains images of various classes of all the four datasets (BloodMNIST, BreastMNIST, PathMNIST, RetinaMNIST) used

## Running Codes

**Clone the project repository:**

``` git clone https://github.com/arindam369/MedMNIST-ViT.git ```   ``` cd MedMNIST-ViT ```

*Run BloodMNIST.ipynb, BreastMNIST.ipynb, PathMNIST.ipynb, RetinaMNIST.ipynb files to view the result of our model on the respective datasets. ``gradcam`` directory contains the codes of visualising GradCAM Analysis on the respective datasets using our proposed model. Use the images of the ``images`` directory to perform GradCAM Analysis.*

## Datasets

The datasets utilized in this study can be found at: [albertvillanova/medmnist-v2](https://huggingface.co/datasets/albertvillanova/medmnist-v2) | [MedMNIST](https://medmnist.com)

## Citation

If you find this work helpful, consider citing our study:

```

@article{Halder2024,

   title={Implementing vision transformer for classifying 2D biomedical images},

   author={Halder, Arindam and Gharami, Sanghita and Sadhu, Priyangshu and Singh, Pawan Kumar and Woźniak, Marcin and Ijaz, Muhammad Fazal},

   journal={Scientific Reports},

   volume={14},

   number={1},

   pages={12567},

   year={2024},

   month={may},

   day={31},

   issn={2045-2322},

   doi={10.1038/s41598-024-63094-9},

   url={https://doi.org/10.1038/s41598-024-63094-9}

}

```