Metadata-Version: 2.1
Name: decimer
Version: 2.7.1
Summary: DECIMER 2.6.0: Deep Learning for Chemical Image Recognition using Efficient-Net V2 + Transformer
Home-page: https://github.com/Kohulan/DECIMER-Image_Transformer
Author: Kohulan Rajan
Author-email: kohulan.rajan@uni-jena.de
Maintainer: Kohulan Rajan, Otto Brinkhaus 
Maintainer-email: kohulan.rajan@uni-jena.de, otto.brinkhaus@uni-jena.de
License: MIT
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.5
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: tensorflow<=2.15.0,>=2.12.0
Requires-Dist: opencv-python
Requires-Dist: pystow
Requires-Dist: pillow-heif
Requires-Dist: efficientnet
Requires-Dist: selfies
Requires-Dist: pyyaml

<div align="center">

# 🧪 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>

[![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg?style=for-the-badge)](https://opensource.org/licenses/MIT)
[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg?style=for-the-badge)](https://GitHub.com/Kohulan/DECIMER-Image_Transformer/graphs/commit-activity)
[![GitHub issues](https://img.shields.io/github/issues/Kohulan/DECIMER-Image_Transformer.svg?style=for-the-badge)](https://GitHub.com/Kohulan/DECIMER-Image_Transformer/issues/)
[![GitHub contributors](https://img.shields.io/github/contributors/Kohulan/DECIMER-Image_Transformer.svg?style=for-the-badge)](https://GitHub.com/Kohulan/DECIMER-Image_Transformer/graphs/contributors/)
[![tensorflow](https://img.shields.io/badge/TensorFlow-2.10.1-FF6F00.svg?style=for-the-badge&logo=tensorflow)](https://www.tensorflow.org)
[![DOI](https://zenodo.org/badge/293572361.svg)](https://zenodo.org/badge/latestdoi/293572361)
[![Documentation Status](https://readthedocs.org/projects/decimer-image-transformer/badge/?version=latest&style=for-the-badge)](https://decimer-image-transformer.readthedocs.io/en/latest/?badge=latest)
[![GitHub release](https://img.shields.io/github/release/Kohulan/DECIMER-Image_Transformer.svg?style=for-the-badge)](https://GitHub.com/Kohulan/DECIMER-Image_Transformer/releases/)
[![PyPI version fury.io](https://badge.fury.io/py/decimer.svg?style=for-the-badge)](https://pypi.python.org/pypi/decimer/)

</div>

---

## 📚 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)

---

## 🔬 Abstract

<div style="background-color: #f0f0f0; padding: 15px; border-radius: 10px;">

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!

</div>

---

## 🧠 Method and Model Changes

<table>
  <tr>
    <td width="50%">
      <h3>🖼️ Image Feature Extraction</h3>
      <p>Now utilizing EfficientNet-V2 for superior image analysis</p>
    </td>
    <td width="50%">
      <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

---

## 💻 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
```

---

## 🎮 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}")
```

---

## ✍️ DECIMER - Hand-drawn Model

<div style="background-color: #e6f7ff; padding: 15px; border-radius: 10px;">

🌟 **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)

</div>

---

## 📜 Citation

<div style="background-color: #f9f9f9; padding: 15px; border-radius: 10px;">

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).

</div>

---

## 🙏 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>

---

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

<p align="center">
  <img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/raw/master/assets/DECIMER.gif" width="300">
</p>

---

## 🌐 Project Website

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

---

## 🏫 Research Group

<p align="center">
  <a href="https://cheminf.uni-jena.de">
    <img src="https://github.com/Kohulan/DECIMER-Image-to-SMILES/blob/master/assets/CheminfGit.png" width="300">
  </a>
</p>

---

<div align="center">

### 📊 Project Analytics

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

</div>
