{"id":20893206,"url":"https://github.com/keiserlab/chemprobe","last_synced_at":"2026-03-02T09:02:22.757Z","repository":{"id":190695074,"uuid":"572700822","full_name":"keiserlab/chemprobe","owner":"keiserlab","description":null,"archived":false,"fork":false,"pushed_at":"2024-08-28T00:03:22.000Z","size":220,"stargazers_count":1,"open_issues_count":3,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-01-05T03:40:04.310Z","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":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/keiserlab.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":"2022-11-30T21:03:34.000Z","updated_at":"2024-08-28T00:03:25.000Z","dependencies_parsed_at":null,"dependency_job_id":"92ebbf19-22a4-4864-be93-3ad1031c42f3","html_url":"https://github.com/keiserlab/chemprobe","commit_stats":null,"previous_names":["keiserlab/chemprobe"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/keiserlab/chemprobe","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fchemprobe","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fchemprobe/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fchemprobe/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fchemprobe/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/keiserlab","download_url":"https://codeload.github.com/keiserlab/chemprobe/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/keiserlab%2Fchemprobe/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29996271,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-02T01:47:34.672Z","status":"online","status_checked_at":"2026-03-02T02:00:07.342Z","response_time":60,"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":"2024-11-18T10:14:58.927Z","updated_at":"2026-03-02T09:02:22.733Z","avatar_url":"https://github.com/keiserlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# chemprobe \n[![DOI](https://zenodo.org/badge/572700822.svg)](https://zenodo.org/doi/10.5281/zenodo.13381833)\n\n## installation\nRequires `python\u003c=3.11`\n\nTo access model \u0026 dataset modules:\n```\npip install chemprobe\n```\nTo access scripts for preprocessing/training/inference you must install from source:\n```\ngit clone https://github.com/keiserlab/chemprobe.git\ncd chemprobe\n# use a virutal env...\n# conda activate env\npip install .\n```\n\n## download data\nRequired to run inference\n```\nbash download_data.sh\n```\n\n## preprocess\nRequired to run inference\n```\npython preprocess.py \\\n    --data_path ../data\n```\n\n## train\n```\npython train.py \\\n    --name TEST \\\n    --exp film \\\n    --fold 0 \\\n    --n_blocks 4 \\\n    --data_path ../data/preprocessed \\\n    --batch_size 16384 \\\n    --gpus 0,1,2,3 \\\n    --num_workers 4 \\\n    --lr 1e-3\n```\n\npermuted label model\n```\npython train.py \\\n--study_path /scratch/wconnell/danger/chemprobe/optuna/exp=film/fold=0/ \\\n--data_path ../data/preprocessed \\\n--name perm-fold=0 \\\n--exp film \\\n--fold 0 \\\n--max_epochs 5 \\\n--batch_size 16384 \\\n--gpus 3, \\\n--permute_labels\n```\n\n## optimize\n```\npython optimize.py \\\n    --study_path /srv/danger/scratch/wconnell/chemprobe/optuna/ \\\n    --data_path ../data/preprocessed \\\n    --exp film \\\n    --fold 0 \\\n    --n_trials 20 \\\n    --prune \\\n    --batch_size 16384 \\\n    --gpus 1,\n```\n\n## predict\n```\npython predict.py \\\n    --cpds neratinib \\ # Do not specify to run on all compounds\n    --data_path ../data/your_data/ \\\n    --attribute \\ # optional to run attribution\n    --batch_size 128 \\\n    --gpus 2,\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeiserlab%2Fchemprobe","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkeiserlab%2Fchemprobe","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkeiserlab%2Fchemprobe/lists"}