{"id":17255130,"url":"https://github.com/unixjunkie/tox21baseline","last_synced_at":"2025-10-09T05:34:41.286Z","repository":{"id":144782790,"uuid":"191710592","full_name":"UnixJunkie/tox21baseline","owner":"UnixJunkie","description":"mirror of https://spotlite.nih.gov/opensource/tox21baseline.git","archived":false,"fork":false,"pushed_at":"2019-06-13T08:07:52.000Z","size":19210,"stargazers_count":1,"open_issues_count":0,"forks_count":2,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-09-05T11:40:43.641Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://spotlite.nih.gov/opensource/tox21baseline","language":"Java","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/UnixJunkie.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":"2019-06-13T07:12:03.000Z","updated_at":"2022-07-15T18:25:41.000Z","dependencies_parsed_at":null,"dependency_job_id":"1e2e5b08-ed2d-4ba4-b191-fe1d16bd2458","html_url":"https://github.com/UnixJunkie/tox21baseline","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/UnixJunkie/tox21baseline","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Ftox21baseline","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Ftox21baseline/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Ftox21baseline/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Ftox21baseline/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UnixJunkie","download_url":"https://codeload.github.com/UnixJunkie/tox21baseline/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UnixJunkie%2Ftox21baseline/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279000743,"owners_count":26082932,"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":"2025-10-09T02:00:07.460Z","response_time":59,"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":"2024-10-15T07:10:46.326Z","updated_at":"2025-10-09T05:34:41.242Z","avatar_url":"https://github.com/UnixJunkie.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"The Tox21 Challenge baseline models\n===================================\n\nThis repository contains a simple implementation of the [naive\nBayes](http://en.wikipedia.org/wiki/Naive_Bayes_classifier) classifier\nto provide baseline models for the 12 datasets in the [Tox21\nChallenge](https://tripod.nih.gov/tox21/challenge). The \nimplementation makes use of [LyChI](https://github.com/ncats/lychi)\nfor structure standardization and\n[PCFP](https://bitbucket.org/caodac/pcfp) for descriptor/feature\nextraction. Please note that this code is for demonstration\npurposes only; we make no claims as to its validity or correctness. We\ndo, however, encourage you to apply the models as-is (see below for\ninstructions) and submit the results to get a feel for what to\nexpect.\n\n\nCompiling the code\n==================\n\nThe code is self-contained in that all you need is a recent version of\nthe [Java](http://www.oracle.com/technetwork/java/) development kit (e.g.,\nJDK 6+) and [Apache ant](http://ant.apache.org). To compile the code,\nsimply type ```ant``` at the command line. This step is optional as\nthe code is automatically compiled when any of the commands below is\ninvoked.\n\n\nTraining the classifier\n=======================\n\nThe code comes bundled with prebuilt models under the ```models```\ndirectory. However, if you want to build new set of models based on\ntweaks you've made to the code, simply type the following on the\ncommand line:\n\n```\nant train\n```\n\nIf all goes well, this command will generate the following 12 files,\none for each respective model. \n\n```\nNR-AHR.props\nNR-AR-LBD.props\nNR-AR.props\nNR-AROMATASE.props\nNR-ER-LBD.props\nNR-ER.props\nNR-PPAR-GAMMA.props\nSR-ARE.props\nSR-ATAD5.props\nSR-HSE.props\nSR-MMP.props\nSR-P53.props\n```\n\nTo test these models, simply move them to the ```models``` directory\n(thereby replacing the old ones) and type ```ant predict``` (see\nbelow) to test out the new models.\n\n\nGenerating predictions\n======================\n\nTo apply the models to test dataset, simply run the following command:\n\n```\nant predict\n```\n\nUpon successful execution, the following files are generated:\n\n```\nNR-AHR.txt\nNR-AR-LBD.txt\nNR-AR.txt\nNR-AROMATASE.txt\nNR-ER-LBD.txt\nNR-ER.txt\nNR-PPAR-GAMMA.txt\nSR-ARE.txt\nSR-ATAD5.txt\nSR-HSE.txt\nSR-MMP.txt\nSR-P53.txt\n```\n\nEach file is in the proper format for [submission]\n(https://tripod.nih.gov/tox21/challenge/submissions.jsp).\n\n\nContact\n=======\n\nFor questions and/or problems with the code, please feel free to\ncontact the Tox21 team at \u003cncats9800tox21challenge@mail.nih.gov\u003e. Good\nluck with the competition!\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Ftox21baseline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Funixjunkie%2Ftox21baseline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Funixjunkie%2Ftox21baseline/lists"}