decimer 2.8.0
DECIMER 2.7.2: Deep Learning for Chemical Image Recognition using Efficient-Net V2 + Transformer
License: MIT
Requires Python: >=3.9

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# 🧪 DECIMER Image Transformer 🖼️

### Deep Learning for Chemical Image Recognition using Efficient-Net V2 + Transformer

<p align="center">
  <img src="https://github.com/Kohulan/DECIMER-Image_Transformer/blob/master/DECIMER_V2.png?raw=true" alt="DECIMER Logo" width="600">
</p>

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## 📚 Table of Contents

- [📝 Abstract](#-abstract)
- [💡 Method and Model Changes](#-method-and-model-changes)
- [⚙️ Installation](#️-installation)
- [🚀 Usage](#-usage)
- [✍️ Hand-drawn Model](#️-decimer---hand-drawn-model)
- [📄 Citation](#-citation)
- [🙏 Acknowledgements](#-acknowledgements)
- [👨‍🔬 Author](#-author-kohulan)
- [🌐 Project Website](#-project-website)
- [🏛️ Research Group](#️-research-group)

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## 📝 Abstract

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  <img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/raw/master/assets/DECIMER.gif" width="350" align="right">
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> The DECIMER 2.2 project tackles the OCSR (Optical Chemical Structure Recognition) challenge using cutting-edge computational intelligence methods. Our goal? To provide an automated, open-source software solution for chemical image recognition.
> 
> We've supercharged DECIMER with Google's TPU (Tensor Processing Unit) to handle datasets of over 1 million images with lightning speed!

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## 💡 Method and Model Changes

<table>
  <tr>
    <td width="50%" align="center">
      <h3>🖼️ Image Feature Extraction</h3>
      <p>Now utilizing EfficientNet-V2 for superior image analysis</p>
    </td>
    <td width="50%" align="center">
      <h3>🔮 SMILES Prediction</h3>
      <p>Employing a state-of-the-art transformer model</p>
    </td>
  </tr>
</table>

### 🚀 Training Enhancements

1. **📦 TFRecord Files** - Lightning-fast data reading
2. **☁️ Google Cloud Buckets** - Efficient cloud storage solution
3. **🔄 TensorFlow Data Pipeline** - Optimized data loading
4. **⚡ TPU Strategy** - Harnessing the power of Google's TPUs

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## ⚙️ Installation

```bash
# Create a conda wonderland
conda create --name DECIMER python=3.10.0 -y
conda activate DECIMER

# Equip yourself with DECIMER
pip install decimer
```

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## 🚀 Usage

```python
from DECIMER import predict_SMILES

# Unleash the power of DECIMER
image_path = "path/to/your/chemical/masterpiece.jpg"
SMILES = predict_SMILES(image_path)
print(f"🎉 Decoded SMILES: {SMILES}")
```

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## ✍️ DECIMER - Hand-drawn Model

> 🌟 **New Feature Alert!** 🌟
> 
> Our latest model brings the magic of AI to hand-drawn chemical structures!
> 
> [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10781330.svg)](https://doi.org/10.5281/zenodo.10781330)

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## 📄 Citation

If DECIMER helps your research, please cite:

1. Rajan K, et al. "DECIMER.ai - An open platform for automated optical chemical structure identification, segmentation and recognition in scientific publications." *Nat. Commun.* 14, 5045 (2023).
2. Rajan, K., et al. "DECIMER 1.0: deep learning for chemical image recognition using transformers." *J Cheminform* 13, 61 (2021).
3. Rajan, K., et al. "Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture," *J Cheminform* 16, 78 (2024).

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## 🙏 Acknowledgements

- A big thank you to [Charles Tapley Hoyt](https://github.com/cthoyt) for his invaluable contributions!
- Powered by Google's TPU Research Cloud (TRC)

<p align="center">
  <img src="https://user-images.githubusercontent.com/30716951/220350828-913e6645-6a0a-403c-bcb8-160d061d4606.png" width="300">
</p>

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## 👨‍🔬 Author: [Kohulan](https://kohulanr.com)

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## 🌐 Project Website

Experience DECIMER in action at [decimer.ai](https://decimer.ai), brilliantly implemented by [Otto Brinkhaus](https://github.com/OBrink)!

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### 🎓 Maintained by the [Kohulan](https://www.kohulanr.com/#) @ Steinbeck Group

<a href="https://cheminf.uni-jena.de">
<img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/blob/master/assets/CheminfGit.png" width="400" alt="Cheminformatics Group"/>
</a>

**[Natural Products Cheminformatics Research Group](https://cheminf.uni-jena.de)**  
Institute for Inorganic and Analytical Chemistry  
Friedrich Schiller University Jena, Germany

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## ⭐ Star History

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[![Star History Chart](https://api.star-history.com/svg?repos=Kohulan/DECIMER-Image_Transformer&type=Date)](https://star-history.com/#Kohulan/DECIMER-Image_Transformer&Date)

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### 📊 Project Analytics

![Repobeats](https://repobeats.axiom.co/api/embed/bf532b7ac0d34137bdea8fbb82986828f86de065.svg "Repobeats analytics image")

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**Made with ❤️ and ☕ for the global chemistry community**

**© 2025 Kohulan @ Steinbeck Lab, Friedrich Schiller University Jena**
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