{"id":18785307,"url":"https://github.com/andreped/adverse-events","last_synced_at":"2025-04-13T12:33:52.827Z","repository":{"id":47469220,"uuid":"366009980","full_name":"andreped/adverse-events","owner":"andreped","description":"IEEE BIBM 2021: Bayesian optimization-guided topic modeling for automatic detection of sepsis-related events from free text","archived":false,"fork":false,"pushed_at":"2023-04-16T19:59:56.000Z","size":75,"stargazers_count":7,"open_issues_count":0,"forks_count":3,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-13T05:36:23.619Z","etag":null,"topics":["adverse-events","bayesian-optimization","classification","data-set","detection","ieee-bibm","latent-dirichlet-allocation","lda","machine-learning","natural-language-processing","sepsis"],"latest_commit_sha":null,"homepage":"","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/andreped.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":"2021-05-10T10:51:53.000Z","updated_at":"2024-08-04T15:46:34.000Z","dependencies_parsed_at":"2024-11-07T20:47:04.361Z","dependency_job_id":"d125602a-c34d-439e-b85c-90d629c54c30","html_url":"https://github.com/andreped/adverse-events","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fadverse-events","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fadverse-events/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fadverse-events/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fadverse-events/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andreped","download_url":"https://codeload.github.com/andreped/adverse-events/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248714740,"owners_count":21149959,"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":["adverse-events","bayesian-optimization","classification","data-set","detection","ieee-bibm","latent-dirichlet-allocation","lda","machine-learning","natural-language-processing","sepsis"],"created_at":"2024-11-07T20:46:15.607Z","updated_at":"2025-04-13T12:33:52.541Z","avatar_url":"https://github.com/andreped.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# adverse-events\n\n[![license](https://img.shields.io/github/license/DAVFoundation/captain-n3m0.svg?style=flat-square)](https://github.com/DAVFoundation/captain-n3m0/blob/master/LICENSE)\n\nThis repository contains the source code related to the manuscript _\"Preliminary Processing and Analysis of an Adverse Event Dataset for Detecting Sepsis-Related Events\"_, presented at the [IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2021)](http://ieeebibm.org/BIBM2021/).\n\nA PDF of the published paper can be accessed [here](https://ntnuopen.ntnu.no/ntnu-xmlui/bitstream/handle/11250/2979827/B579_9996.pdf?sequence=2\u0026isAllowed=y). See [here](https://github.com/andreped/adverse-events/releases/tag/v1.0) to download the exact version of the source code used in the publication (v1.0).\n\n## [Usage](https://github.com/andreped/adverse-events#usage)\n\n1) Clone repo:\n    \u003e git clone https://github.com/andreped/adverse-events.git\n\n2) Create virtual environment, activate it, and install dependencies:\n    \u003e cd adverse-events/python  \n    \u003e virtualenv -ppython3 venv --clear  \n    \u003e source venv/bin/activate  \n    \u003e pip install -r /path/to/requirements.txt\n\n3) Create the project structure as defined [below](https://github.com/andreped/adverse-events#project-structure).\n\n4) Run scripts for training and evaluating different classifier models:\n    \u003e python main.py misc/default-params.ini\n\nDifferent parameters relevant for the analysis, building of models, evaluation, plotting results, and similar, may be modified in the INI-file.\n\n## [Project structure](https://github.com/andreped/adverse-events#project-structure)\n\n    └── adverse-events\n        ├── python\n        │   ├── multi-class\n        │   ├── topic-analysis\n        │   ├── utils\n        │   └── ...\n        ├── data\n        │   ├── EQS_files\n        │   ├── file-with-all-notes.csv\n        │   └── file_with_annotated_notes.csv\n        └── output\n            ├── history\n            ├── models\n            └── figures\n\n## [How to cite](https://github.com/andreped/adverse-events#how-to-cite)\n\nIf you use parts of the source code in your research, please, cite this publication:\n\n```\n@INPROCEEDINGS{yan2021sepsis,\n    author={Yan, Melissa Y. and Høvik, Lise Husby and Pedersen, André and Gustad, Lise Tuset and Nytrø, Øystein},\n    booktitle={2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)},\n    title={Preliminary Processing and Analysis of an Adverse Event Dataset for Detecting Sepsis-Related Events},\n    year={2021},\n    pages={1605-1610},\n    doi={10.1109/BIBM52615.2021.9669410}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandreped%2Fadverse-events","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandreped%2Fadverse-events","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandreped%2Fadverse-events/lists"}