{"id":21275057,"url":"https://github.com/maayanlab/graph-dr","last_synced_at":"2025-07-11T07:30:34.370Z","repository":{"id":39854569,"uuid":"124105993","full_name":"MaayanLab/Graph-DR","owner":"MaayanLab","description":"Benchmarks of dimensionality reduction algorithms","archived":false,"fork":false,"pushed_at":"2023-03-24T21:55:05.000Z","size":32568,"stargazers_count":4,"open_issues_count":2,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-06T01:32:24.358Z","etag":null,"topics":["autoencoder","cytoscape","dimensionality-reduction","force-layout","graph-algorithms","graph-theory","manifold-learning"],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MaayanLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-03-06T16:26:30.000Z","updated_at":"2023-11-30T07:59:47.000Z","dependencies_parsed_at":"2024-11-21T09:39:15.053Z","dependency_job_id":null,"html_url":"https://github.com/MaayanLab/Graph-DR","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MaayanLab/Graph-DR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FGraph-DR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FGraph-DR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FGraph-DR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FGraph-DR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MaayanLab","download_url":"https://codeload.github.com/MaayanLab/Graph-DR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2FGraph-DR/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":264756298,"owners_count":23659299,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["autoencoder","cytoscape","dimensionality-reduction","force-layout","graph-algorithms","graph-theory","manifold-learning"],"created_at":"2024-11-21T09:27:12.665Z","updated_at":"2025-07-11T07:30:30.552Z","avatar_url":"https://github.com/MaayanLab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"Graph-DR: Benchmarking of dimensionality reduction algorithms\n==============\n\nA series of Jupyter Notebooks experimenting on different dimensionality reduction algorithms and their performance on the [MNIST dataset](http://yann.lecun.com/exdb/mnist/). \n\nGet started\n------------\n\nThere are two options to run the notebooks in this repository:\n\n### 1. Docker\n\nTo start running the docker image:\n\n    docker run -it -p 8888:8888 maayanlab/graph-dr:2019\n\nNext, you can open a browser and go to http://localhost:8888. You will be required to enter the token to access the notebook server, which can be found in the terminal running the Docker image.\n\n\n### 2. virtualenv\n\nThe recommended way to run these notebooks live is to set up a isolated Python envrionment using [virtualenv](https://virtualenv.pypa.io/en/stable/), after cloning this repository:\n\n    git clone https://github.com/MaayanLab/Graph-DR.git\n    cd Graph-DR/\n\nRun the following to set up a Python virtural environment:\n\n    virtualenv venv\n\nThen activate the virtural environment and install the required Python packages:\n\n    source venv/bin/activate\n    pip install -r requirements.txt\n\nNext, you can start a Jupyter server:\n\n    jupyter notebook\n\nOther dependencies\n------------\n\nSome code blocks in the notebooks require [Cytoscape](http://www.cytoscape.org/) (\u003e3.5.1) to be running as the background. \n\nTo run the firework layout, you will also need to install the a Cytoscape app [AllegroLayout](https://www.dropbox.com/s/uwcpjes6vv212fm/allegrolayout-2.2.2.jar?dl=0). Once the jar file is downloaded, go to `Apps` -\u003e `Install from File` -\u003e open the jar file.\n\n\nReferences\n------------\n\n+ [Making sense of principal component analysis, eigenvectors \u0026 eigenvalues](https://stats.stackexchange.com/questions/2691/making-sense-of-principal-component-analysis-eigenvectors-eigenvalues)\n+ [MNIST For ML Beginners](https://www.tensorflow.org/get_started/mnist/beginners)\n+ [Visualizing MNIST: An Exploration of Dimensionality Reduction](http://colah.github.io/posts/2014-10-Visualizing-MNIST/)\n+ [Tensorflow Embedding Projector](http://projector.tensorflow.org/)\n+ [van der Maaten's t-SNE page](http://lvdmaaten.github.io/tsne/)\n+ [van der Maaten et al.: Dimensionality Reduction: A Comparative Review](https://www.tilburguniversity.edu/upload/59afb3b8-21a5-4c78-8eb3-6510597382db_TR2009005.pdf)\n+ [van der Maaten: Learning a Parametric Embedding by Preserving Local Structure](http://lvdmaaten.github.io/publications/papers/AISTATS_2009.pdf)\n+ [Kokiopoulou and Saad: Enhanced graph-based dimensionality reduction with repulsion Laplaceans](http://www.sciencedirect.com/science/article/pii/S0031320309001460)\n+ [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://arxiv.org/abs/1802.03426)\n+ [Unsupervised learning: the curious pupil](https://deepmind.com/blog/unsupervised-learning/)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fgraph-dr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaayanlab%2Fgraph-dr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fgraph-dr/lists"}