{"id":22017353,"url":"https://github.com/kohulan/decimer-image_transformer","last_synced_at":"2025-12-02T22:05:16.916Z","repository":{"id":45077587,"uuid":"293572361","full_name":"Kohulan/DECIMER-Image_Transformer","owner":"Kohulan","description":"DECIMER Image Transformer is a deep-learning-based tool designed for automated recognition of chemical structure images. 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align=\"center\"\u003e\n\n# 🧪 DECIMER Image Transformer 🖼️\n\n### Deep Learning for Chemical Image Recognition using Efficient-Net V2 + Transformer\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/Kohulan/DECIMER-Image_Transformer/blob/master/DECIMER_V2.png?raw=true\" alt=\"DECIMER Logo\" width=\"600\"\u003e\n\u003c/p\u003e\n\n[![License](https://img.shields.io/badge/License-MIT%202.0-blue.svg?style=for-the-badge)](https://opensource.org/licenses/MIT)\n[![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)\n[![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/)\n[![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/)\n[![tensorflow](https://img.shields.io/badge/TensorFlow-2.10.1-FF6F00.svg?style=for-the-badge\u0026logo=tensorflow)](https://www.tensorflow.org)\n[![Model Card](https://img.shields.io/badge/Model_Card-DECIMER-9cf.svg?style=for-the-badge)](https://zenodo.org/records/8300489)\n[![DOI](https://zenodo.org/badge/293572361.svg)](https://zenodo.org/badge/latestdoi/293572361)\n[![Documentation Status](https://readthedocs.org/projects/decimer-image-transformer/badge/?version=latest\u0026style=for-the-badge)](https://decimer-image-transformer.readthedocs.io/en/latest/?badge=latest)\n[![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/)\n[![PyPI version fury.io](https://badge.fury.io/py/decimer.svg?style=for-the-badge)](https://pypi.python.org/pypi/decimer/)\n\n\u003c/div\u003e\n\n---\n\n## 📚 Table of Contents\n\n- [📝 Abstract](#-abstract)\n- [💡 Method and Model Changes](#-method-and-model-changes)\n- [⚙️ Installation](#️-installation)\n- [🚀 Usage](#-usage)\n- [✍️ Hand-drawn Model](#️-decimer---hand-drawn-model)\n- [📄 Citation](#-citation)\n- [🙏 Acknowledgements](#-acknowledgements)\n- [👨‍🔬 Author](#-author-kohulan)\n- [🌐 Project Website](#-project-website)\n- [🏛️ Research Group](#️-research-group)\n\n---\n\n## 📝 Abstract\n\n\u003cdiv align=\"center\"\u003e\n  \u003cimg src=\"https://github.com/Kohulan/DECIMER-Image-to-SMILES/raw/master/assets/DECIMER.gif\" width=\"350\" align=\"right\"\u003e\n\u003c/div\u003e\n\n\u003e 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.\n\u003e \n\u003e We've supercharged DECIMER with Google's TPU (Tensor Processing Unit) to handle datasets of over 1 million images with lightning speed!\n\n---\n\n## 💡 Method and Model Changes\n\n\u003ctable\u003e\n  \u003ctr\u003e\n    \u003ctd width=\"50%\" align=\"center\"\u003e\n      \u003ch3\u003e🖼️ Image Feature Extraction\u003c/h3\u003e\n      \u003cp\u003eNow utilizing EfficientNet-V2 for superior image analysis\u003c/p\u003e\n    \u003c/td\u003e\n    \u003ctd width=\"50%\" align=\"center\"\u003e\n      \u003ch3\u003e🔮 SMILES Prediction\u003c/h3\u003e\n      \u003cp\u003eEmploying a state-of-the-art transformer model\u003c/p\u003e\n    \u003c/td\u003e\n  \u003c/tr\u003e\n\u003c/table\u003e\n\n### 🚀 Training Enhancements\n\n1. **📦 TFRecord Files** - Lightning-fast data reading\n2. **☁️ Google Cloud Buckets** - Efficient cloud storage solution\n3. **🔄 TensorFlow Data Pipeline** - Optimized data loading\n4. **⚡ TPU Strategy** - Harnessing the power of Google's TPUs\n\n---\n\n## ⚙️ Installation\n\n```bash\n# Create a conda wonderland\nconda create --name DECIMER python=3.10.0 -y\nconda activate DECIMER\n\n# Equip yourself with DECIMER\npip install decimer\n```\n\n---\n\n## 🚀 Usage\n\n```python\nfrom DECIMER import predict_SMILES\n\n# Unleash the power of DECIMER\nimage_path = \"path/to/your/chemical/masterpiece.jpg\"\nSMILES = predict_SMILES(image_path)\nprint(f\"🎉 Decoded SMILES: {SMILES}\")\n```\n\n---\n\n## ✍️ DECIMER - Hand-drawn Model\n\n\u003e 🌟 **New Feature Alert!** 🌟\n\u003e \n\u003e Our latest model brings the magic of AI to hand-drawn chemical structures!\n\u003e \n\u003e [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10781330.svg)](https://doi.org/10.5281/zenodo.10781330)\n\n---\n\n## 📄 Citation\n\nIf DECIMER helps your research, please cite:\n\n1. 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).\n2. Rajan, K., et al. \"DECIMER 1.0: deep learning for chemical image recognition using transformers.\" *J Cheminform* 13, 61 (2021).\n3. Rajan, K., et al. \"Advancements in hand-drawn chemical structure recognition through an enhanced DECIMER architecture,\" *J Cheminform* 16, 78 (2024).\n\n---\n\n## 🙏 Acknowledgements\n\n- A big thank you to [Charles Tapley Hoyt](https://github.com/cthoyt) for his invaluable contributions!\n- Powered by Google's TPU Research Cloud (TRC)\n\n\u003cp align=\"center\"\u003e\n  \u003cimg src=\"https://user-images.githubusercontent.com/30716951/220350828-913e6645-6a0a-403c-bcb8-160d061d4606.png\" width=\"300\"\u003e\n\u003c/p\u003e\n\n---\n\n## 👨‍🔬 Author: [Kohulan](https://kohulanr.com)\n\n---\n\n## 🌐 Project Website\n\nExperience DECIMER in action at [decimer.ai](https://decimer.ai), brilliantly implemented by [Otto Brinkhaus](https://github.com/OBrink)!\n\n---\n\n\u003cdiv align=\"center\"\u003e\n\n### 🎓 Maintained by the [Kohulan](https://www.kohulanr.com/#) @ Steinbeck Group\n\n\u003ca href=\"https://cheminf.uni-jena.de\"\u003e\n\u003cimg src=\"https://github.com/Kohulan/DECIMER-Image-to-SMILES/blob/master/assets/CheminfGit.png\" width=\"400\" alt=\"Cheminformatics Group\"/\u003e\n\u003c/a\u003e\n\n**[Natural Products Cheminformatics Research Group](https://cheminf.uni-jena.de)**  \nInstitute for Inorganic and Analytical Chemistry  \nFriedrich Schiller University Jena, Germany\n\n---\n## ⭐ Star History\n\n\u003cdiv align=\"center\"\u003e\n\n[![Star History Chart](https://api.star-history.com/svg?repos=Kohulan/DECIMER-Image_Transformer\u0026type=Date)](https://star-history.com/#Kohulan/DECIMER-Image_Transformer\u0026Date)\n\n\u003c/div\u003e\n\n---\n\n\u003cdiv align=\"center\"\u003e\n\n### 📊 Project Analytics\n\n![Repobeats](https://repobeats.axiom.co/api/embed/bf532b7ac0d34137bdea8fbb82986828f86de065.svg \"Repobeats analytics image\")\n\n\u003c/div\u003e\n\n\u003cdiv align=\"center\"\u003e\n  \n**Made with ❤️ and ☕ for the global chemistry community**\n\n**© 2025 Kohulan @ Steinbeck Lab, Friedrich Schiller University Jena**\n---\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkohulan%2Fdecimer-image_transformer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkohulan%2Fdecimer-image_transformer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkohulan%2Fdecimer-image_transformer/lists"}