{"id":22731054,"url":"https://github.com/genentech/pascient","last_synced_at":"2025-04-14T00:32:42.187Z","repository":{"id":259586279,"uuid":"877640179","full_name":"Genentech/pascient","owner":"Genentech","description":null,"archived":false,"fork":false,"pushed_at":"2024-10-25T04:00:11.000Z","size":3393,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2024-10-26T18:47:35.765Z","etag":null,"topics":[],"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":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Genentech.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-10-24T01:39:20.000Z","updated_at":"2024-10-25T12:17:21.000Z","dependencies_parsed_at":"2024-10-26T18:47:41.570Z","dependency_job_id":"19f1336e-dd21-499a-8241-96c746e3680d","html_url":"https://github.com/Genentech/pascient","commit_stats":null,"previous_names":["genentech/pascient"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpascient","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpascient/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpascient/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fpascient/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/pascient/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":229117070,"owners_count":18022819,"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":[],"created_at":"2024-12-10T19:19:16.682Z","updated_at":"2025-04-14T00:32:42.181Z","avatar_url":"https://github.com/Genentech.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PaSCient: Learning multi-cellular representations of single-cell transcriptomics data enables characterization of patient-level disease states\n\n![](figure1.jpeg)\n\n## Setup environment\n\n```\nconda create -n pascient python=3.11\n```\n\n## Install\n```\npip install -r requirements.txt\n```\n\n## Train a PaSCient model\n\n\n`cd /pascient/scripts/`\n\n```\nHYDRA_FULL_ERROR=1 python train.py data.persistent_workers=True data.multiprocessing_context=null data.num_workers=12 experiment=pascient_multilabel paths.tiledb_dir=YOUR_PATH_TO_YOUR_TILEDB\n```\n\nYou will need to provide the path to your tiledb.\n\n## PaSCient inference\n\nWe provide a notebook with examples on how to run PaSCient on your data in `pascient/notebooks/paper_figures/model_inference_example.ipynb`\n\n## Request model weights\n\nModel weights are available upon request to `debroue1@gene.com`\n\n\n## Figures reproduction\n\nFigures were generated using the notebooks in  `pascient/notebooks/paper_figures/`\n\n- `UMAP.ipynb` reproduces Figure 3 of the paper\n- `IG.ipynb` reproduces Figure 4 of the paper\n- `severity.ipynb` reproduces Figure 5 of the paper\n\n\n## Contact\n\nIf you have any questions, please contact Tianyu Liu (tianyu.liu@yale.edu) or Edward De Brouwer (debroue1@gene.com).\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fpascient","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fpascient","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fpascient/lists"}