{"id":31805897,"url":"https://github.com/theislab/disent","last_synced_at":"2025-10-11T03:02:13.532Z","repository":{"id":54077564,"uuid":"220269541","full_name":"theislab/disent","owner":"theislab","description":"Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data","archived":false,"fork":false,"pushed_at":"2021-05-08T12:21:52.000Z","size":31604,"stargazers_count":6,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2024-12-30T12:46:52.467Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/theislab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-11-07T15:33:05.000Z","updated_at":"2024-01-21T18:08:40.000Z","dependencies_parsed_at":"2022-08-13T06:31:19.053Z","dependency_job_id":null,"html_url":"https://github.com/theislab/disent","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/theislab/disent","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fdisent","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fdisent/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fdisent/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fdisent/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/theislab","download_url":"https://codeload.github.com/theislab/disent/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/theislab%2Fdisent/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279005972,"owners_count":26084009,"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","status":"online","status_checked_at":"2025-10-11T02:00:06.511Z","response_time":55,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2025-10-11T03:00:17.460Z","updated_at":"2025-10-11T03:02:13.519Z","avatar_url":"https://github.com/theislab.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data\n\nThe pdf for the paper can be found [here](https://github.com/theislab/disent/raw/master/paper.pdf).\n\n\n### Usage\n\nReproducing results from Jupyter Notebooks:\n* JN1_train.ipynb - loads, normalizes and trains the data\n* JN2_kang_analysis.ipynb - further analyses the trained model for Kang dataset. It calculates both types of disentanglement scores and also visualizes the latent space as well as gene-feature space plots.\n* JN3_dentate_analysis.ipynb - further analyses the trained model for Dentate Gyrus dataset.\n* JN4_Out of Distribution Prediction.ipynb - implements OOD Prediction and analyses the results further\n* Model Comparisons folder provides the notebooks to reproduce the model architecture comparison plots.\n\n### Misc\n* The **environment.yml** file specifies the conda environment in which the project was run.\n* Data can be accessed from [here](https://drive.google.com/open?id=1ywXG0K-_nuqnFL8u3x4klsPNOrEdeg27)\n\n\n## Reference\n\nplease consider citing\n\n\n```\n@inproceedings{lotfollahi2020out,\n  title={Out-of-distribution prediction with disentangled representations for single-cell RNA sequencing data},\n  author={Lotfollahi, Mohammad and Dony, Leander and Agarwala, Harshita and Theis, Fabian},\n  booktitle={ICML 2020 Workshop on Computational Biology (WCB) Proceedings Paper},\n  volume={37},\n  year={2020}\n}\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fdisent","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftheislab%2Fdisent","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftheislab%2Fdisent/lists"}