{"id":13737523,"url":"https://github.com/zhangxiaoyu11/OmiEmbed","last_synced_at":"2025-05-08T14:31:57.580Z","repository":{"id":40478373,"uuid":"334077812","full_name":"zhangxiaoyu11/OmiEmbed","owner":"zhangxiaoyu11","description":"Multi-task deep learning framework for multi-omics data 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OmiEmbed\n***Please also have a look at our brand new omics-to-omics DL freamwork 👀:***\n[OmiTrans](https://github.com/zhangxiaoyu11/OmiTrans)\n\n[![DOI](https://zenodo.org/badge/334077812.svg)](https://zenodo.org/badge/latestdoi/334077812)\n[![Codacy Badge](https://app.codacy.com/project/badge/Grade/ce304bf91b534e26b310b3c50072e8ae)](https://www.codacy.com/gh/zhangxiaoyu11/OmiEmbed/dashboard?utm_source=github.com\u0026amp;utm_medium=referral\u0026amp;utm_content=zhangxiaoyu11/OmiEmbed\u0026amp;utm_campaign=Badge_Grade)\n[![GitHub license](https://img.shields.io/github/license/Naereen/StrapDown.js.svg)](https://github.com/zhangxiaoyu11/OmiEmbed/blob/main/LICENSE)\n![Safe](https://img.shields.io/badge/Stay-Safe-red?logo=data:image/svg%2bxml;base64,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)\n[![GitHub Repo stars](https://img.shields.io/github/stars/zhangxiaoyu11/OmiEmbed?style=social)](https://github.com/zhangxiaoyu11/OmiEmbed/stargazers)\n[![GitHub forks](https://img.shields.io/github/forks/zhangxiaoyu11/OmiEmbed?style=social)](https://github.com/zhangxiaoyu11/OmiEmbed/network/members)\n\n**OmiEmbed: A Unified Multi-task Deep Learning Framework for Multi-omics Data**\n\n**Xiaoyu Zhang** (x.zhang18@imperial.ac.uk)\n\nData Science Institute, Imperial College London\n\n## Introduction\n\nOmiEmbed is a unified framework for deep learning-based omics data analysis, which supports:\n\n1.  Multi-omics integration\n2.  Dimensionality reduction\n3.  Omics embedding learning\n4.  Tumour type classification\n5.  Phenotypic feature reconstruction\n6.  Survival prediction\n7.  Multi-task learning for aforementioned tasks\n\nPaper Link: [https://doi.org/10.3390/cancers13123047](https://doi.org/10.3390/cancers13123047)\n\n## Getting Started\n\n### Prerequisites\n-   CPU or NVIDIA GPU + CUDA CuDNN\n-   [Python](https://www.python.org/downloads) 3.6+\n-   Python Package Manager\n    -   [Anaconda](https://docs.anaconda.com/anaconda/install) 3 (recommended)\n    -   or [pip](https://pip.pypa.io/en/stable/installing/) 21.0+\n-   Python Packages\n    -   [PyTorch](https://pytorch.org/get-started/locally) 1.2+\n    -   TensorBoard 1.10+\n    -   Tables 3.6+\n    -   scikit-survival 0.6+\n    -   prefetch-generator 1.0+\n-   [Git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) 2.7+\n\n### Installation\n-   Clone the repo\n```bash\ngit clone https://github.com/zhangxiaoyu11/OmiEmbed.git\ncd OmiEmbed\n```\n-   Install the dependencies\n    -   For conda users  \n    ```bash\n    conda env create -f environment.yml\n    conda activate omiembed\n    ```\n    -   For pip users\n    ```bash\n    pip install -r requirements.txt\n    ```\n\n### Try it out\n-   Train and test using the built-in sample dataset with the default settings\n```bash\npython train_test.py\n```\n-   Check the output files\n```bash\ncd checkpoints/test/\n```\n-   Visualise the metrics and losses\n```bash\ntensorboard --logdir=tb_log --bind_all\n```\n\n## Citation\nIf you use this code in your research, please cite our paper.\n```bibtex\n@Article{OmiEmbed2021,\n    AUTHOR = {Zhang, Xiaoyu and Xing, Yuting and Sun, Kai and Guo, Yike},\n    TITLE = {OmiEmbed: A Unified Multi-Task Deep Learning Framework for Multi-Omics Data},\n    JOURNAL = {Cancers},\n    VOLUME = {13},\n    YEAR = {2021},\n    NUMBER = {12},\n    ARTICLE-NUMBER = {3047},\n    ISSN = {2072-6694},\n    DOI = {10.3390/cancers13123047}\n}\n```\n\n## OmiTrans\n***Please also have a look at our brand new omics-to-omics DL freamwork 👀:***\n[OmiTrans](https://github.com/zhangxiaoyu11/OmiTrans)\n\n## License\nThis source code is licensed under the [MIT](https://github.com/zhangxiaoyu11/OmiEmbed/blob/main/LICENSE) license.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzhangxiaoyu11%2FOmiEmbed","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzhangxiaoyu11%2FOmiEmbed","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzhangxiaoyu11%2FOmiEmbed/lists"}