{"id":15118933,"url":"https://github.com/genentech/dcdfg","last_synced_at":"2025-09-04T12:33:47.854Z","repository":{"id":72633436,"uuid":"542349328","full_name":"Genentech/dcdfg","owner":"Genentech","description":null,"archived":false,"fork":false,"pushed_at":"2022-10-04T14:06:27.000Z","size":85,"stargazers_count":21,"open_issues_count":1,"forks_count":4,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-09-26T02:01:40.251Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","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.md","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":"2022-09-28T00:58:12.000Z","updated_at":"2024-03-23T22:34:03.000Z","dependencies_parsed_at":"2023-04-15T22:04:37.726Z","dependency_job_id":null,"html_url":"https://github.com/Genentech/dcdfg","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fdcdfg","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fdcdfg/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fdcdfg/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Genentech%2Fdcdfg/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Genentech","download_url":"https://codeload.github.com/Genentech/dcdfg/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":"2024-09-26T01:53:40.583Z","updated_at":"2024-12-10T19:19:18.160Z","avatar_url":"https://github.com/Genentech.png","language":"Python","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"# Differentiable Causal Discovery with Factor Graphs\n\nThis repository contains an implementation of the structure learning method described in [\"Large-Scale Differentiable Causal Discovery of Factor Graphs\"](https://arxiv.org/abs/2206.07824). \n\nIf you find it useful, please consider citing:\n```bibtex\n@inproceedings{Lopez2022largescale,\n  author = {Lopez, Romain and Hütter, Jan-Christian and Pritchard, Jonathan K. and Regev, Aviv}, \n  title = {Large-Scale Differentiable Causal Discovery of Factor Graphs},\n  booktitle = {Advances in Neural Information Processing Systems},\n  year = {2022},\n}\n```\n\n## Requirements\n\nPython 3.9+ is required. To install the requirements:\n```setup\npip install -r requirements.txt\n```\nwandb is required for now (a PR to make remove this requirement is welcome). Follow the steps [here](https://docs.wandb.ai/quickstart).\n\n\n## Running DCD-FG\n\n### SEMs simulations (full usage in files)\n1. 'python make_lowrank_dataset.py'\n2. 'python run_gaussian.py'\n### Biological dataset\n1. 'perturb-cite-seq/0-data-download.ipynb'\n1. 'perturb-cite-seq/1-assignments-vs-variability.ipynb'\n2. 'python run_perturbseq_linear.py'\n\n## Acknowledgments\n- This repository was originally forked from [DCDI](https://github.com/slachapelle/dcdi). Please refer to the license file for more information.\n- Most files in this codebase have been rewritten for:\n1. vectorization and scaling to large graphs\n2. incorporating the semantic of factor graphs\n3. refactoring and implementation in pytorch lightning\n4. implementation of DCD-FG, NOTEARS, NOTEARS-LR and NOBEARS\n- We are grateful to the authors of the baseline methods for releasing their code.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fdcdfg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgenentech%2Fdcdfg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgenentech%2Fdcdfg/lists"}