{"id":19258874,"url":"https://github.com/leechristie/antibiotic-optimisation","last_synced_at":"2026-04-09T17:47:24.206Z","repository":{"id":132437480,"uuid":"148051469","full_name":"leechristie/antibiotic-optimisation","owner":"leechristie","description":"Source for \"Multi-Objective Evolutionary Optimisation of Antibiotic Treatments\" (Ochoa, Christie, Brownlee, \u0026 Hoyle, 2020).","archived":false,"fork":false,"pushed_at":"2018-11-28T10:54:39.000Z","size":9731,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-23T18:16:49.258Z","etag":null,"topics":["antibiotics","computer-science","java","metaheuristics","multiobjective-optimization","optimization","python","python3","research"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1016/j.artmed.2019.101759","language":"Jupyter Notebook","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/leechristie.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":"2018-09-09T17:57:25.000Z","updated_at":"2022-09-04T22:06:37.000Z","dependencies_parsed_at":"2023-11-14T07:30:52.410Z","dependency_job_id":null,"html_url":"https://github.com/leechristie/antibiotic-optimisation","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/leechristie/antibiotic-optimisation","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leechristie%2Fantibiotic-optimisation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leechristie%2Fantibiotic-optimisation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leechristie%2Fantibiotic-optimisation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leechristie%2Fantibiotic-optimisation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/leechristie","download_url":"https://codeload.github.com/leechristie/antibiotic-optimisation/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/leechristie%2Fantibiotic-optimisation/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":269351910,"owners_count":24402678,"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":"2025-08-08T02:00:09.200Z","response_time":72,"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":["antibiotics","computer-science","java","metaheuristics","multiobjective-optimization","optimization","python","python3","research"],"created_at":"2024-11-09T19:14:37.306Z","updated_at":"2025-12-30T21:49:14.084Z","avatar_url":"https://github.com/leechristie.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Antibiotic Optimisation\n\n## Model (antibiotic-model)\n\nA stochastic model for antibiotic resistance.\n\n\u003cdetails\u003e\u003csummary\u003eClick to see documentation...\u003c/summary\u003e\n\n### Example Usage (Model)\n\n`AntibioticModel` can be used directly, giving results to compare to the MATLAB\nreference implementation. The model constructor accepts additional parameters to\nspecify initial bacterial load and random number generator for the simulation.\n\n    int samples = 1000;\n    AntibioticModel model = new AntibioticModel(samples);\n    \n    int[] solution = new int[] {10, 10, 10, 10, 10, 10, 10, 10, 10, 10};\n\n    double fitness = model.evaluate(solution);\n\n### Example Usage (Problem)\n\n`AntibioticProblem` is used to create an `IntegerProblem` instance for jMetal\nalgorithms. Many objectives may be specified.\n\n    int maxIndividualDosage = 60;\n    int maxConcentraition = 60;\n    AntibioticProblem problem = new AntibioticProblem(\n            model,\n            maxIndividualDosage,\n            AntibioticObjective.totalAntibiotic(),\n            AntibioticObjective.overdoseAmount(maxConcentraition),\n            AntibioticObjective.uncuredProportion());\n\n    Algorithm\u003cList\u003cDoubleSolution\u003e\u003e algorithm = ... // jMetal Algorithm usage\n\n\u003c/details\u003e\n\n## Experiments (antibiotic-model-experiments)\n\nDocumentation to follow\n\n## Offline Re-evaluation (antibiotic-offline-reeval)\n\nDocumentation to follow\n\n## Results Post-Processing (results-post-processing)\n\nDocumentation to follow\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fleechristie%2Fantibiotic-optimisation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fleechristie%2Fantibiotic-optimisation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fleechristie%2Fantibiotic-optimisation/lists"}