{"id":35762876,"url":"https://github.com/bionetslab/robust","last_synced_at":"2026-01-07T00:00:36.182Z","repository":{"id":99568183,"uuid":"381036062","full_name":"bionetslab/robust","owner":"bionetslab","description":"ROBUST: Robust disease module mining via enumeration of price-collecting Steiner trees","archived":false,"fork":false,"pushed_at":"2024-02-06T15:55:53.000Z","size":9137,"stargazers_count":5,"open_issues_count":0,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-02-06T16:54:04.782Z","etag":null,"topics":["algorithm"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/bionetslab.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}},"created_at":"2021-06-28T13:10:55.000Z","updated_at":"2023-08-14T07:22:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"e14fc7f6-14f3-4ed2-88fb-7d36f80a11cd","html_url":"https://github.com/bionetslab/robust","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/bionetslab/robust","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Frobust","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Frobust/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Frobust/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Frobust/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/bionetslab","download_url":"https://codeload.github.com/bionetslab/robust/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/bionetslab%2Frobust/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28230229,"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":"2026-01-06T02:00:07.049Z","response_time":56,"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":["algorithm"],"created_at":"2026-01-07T00:00:12.240Z","updated_at":"2026-01-07T00:00:36.163Z","avatar_url":"https://github.com/bionetslab.png","language":"Jupyter Notebook","readme":"# New ROBUST version\n\nWe have developed a new version of ROBUST which corrects for study bias in PPI networks. The new version is available here: https://github.com/bionetslab/robust_bias_aware. Although this version is still fully functional, we recommend using the latest ROBUST version for your research.\n\n# Installation\n\nInstall conda environment as follows (there also exists a environment.yml but it contains more packages than necessary)\n```bash\nconda create --name biosteiner python=3.7\nconda activate biosteiner\nconda install numpy matplotlib pandas networkx pip jupyter\npip install pcst_fast\n```\n\n# Running ROBUST\n\nYou can simply run robust by calling\n```bash\npython robust.py data/human_annotated_PPIs_brain.txt data/ms_seeds.txt ms.graphml 0.25 0.9 30 0.1\n```\nThe positional arguments are:\n```\n[1] file providing the network in the form of an edgelist \n    (tab-separated table, columns 1 \u0026 2 will be used)\n[2] file with the seed genes (if table contains more than \n    one column they must be tab-separated; the first column \n    will be used only)\n[3] path to output file\n[4] initial fraction (alpha)\n[5] reduction factor (beta)\n[6] number of steiner trees to be computed\n[7] threshold (theta)\n```\n\nThe suffix of the path to the output file you specify, determine the format of the output.\nYou can either choose\n- .graphml: A .graphml file is written that contains the following vertex properties: isSeed, significance, nrOfOccurrences, connected_components_id, trees\n- .csv: A .csv file which contains a vertex table with #occurrences, %occurrences, terminal (isSeed) \n- everything else: An edge list\n\n# Evaluating ROBUST\n\nFor a large-scale empirical evaluation of ROBUST, please follow the instructions given here: https://github.com/bionetslab/robust-eval.\n\n# Citing ROBUST\n\nPlease cite ROBUST as follows:\n- J. Bernett, D. Krupke, S. Sadegh1, J. Baumbach, S. P. Fekete, T. Kacprowski, M. List1, D. B. Blumenthal: Robust disease module mining via enumeration of diverse prize-collecting Steiner trees, *Bioinformatics* 38(6), pp. 1600-1606, https://doi.org/10.1093/bioinformatics/btab876.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionetslab%2Frobust","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbionetslab%2Frobust","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbionetslab%2Frobust/lists"}