{"id":27249710,"url":"https://github.com/straymat/bio-medical_ner","last_synced_at":"2026-01-23T15:43:02.614Z","repository":{"id":75579569,"uuid":"139742910","full_name":"strayMat/bio-medical_ner","owner":"strayMat","description":"This repo contains all data and code necessary to reproduce the experiments of ner on some open bio-medical corpora","archived":false,"fork":false,"pushed_at":"2019-03-21T08:49:43.000Z","size":18418,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-11T00:34:35.708Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"SQLPL","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/strayMat.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,"zenodo":null}},"created_at":"2018-07-04T16:05:45.000Z","updated_at":"2019-03-21T08:49:46.000Z","dependencies_parsed_at":"2023-06-13T14:15:27.891Z","dependency_job_id":null,"html_url":"https://github.com/strayMat/bio-medical_ner","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/strayMat/bio-medical_ner","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/strayMat%2Fbio-medical_ner","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/strayMat%2Fbio-medical_ner/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/strayMat%2Fbio-medical_ner/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/strayMat%2Fbio-medical_ner/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/strayMat","download_url":"https://codeload.github.com/strayMat/bio-medical_ner/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/strayMat%2Fbio-medical_ner/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28694830,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-23T14:15:13.573Z","status":"ssl_error","status_checked_at":"2026-01-23T14:09:05.534Z","response_time":59,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2025-04-11T00:31:19.329Z","updated_at":"2026-01-23T15:43:02.606Z","avatar_url":"https://github.com/strayMat.png","language":"SQLPL","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Evaluation of YASET on various bio-medical datasets\n\nThis repo describes the code and the processes used to evaluate [Yaset](http://yaset.readthedocs.io/en/stable/), a neural model for NER on differents datasets. These experiences and their interpretations are precisely discribed in the following paper, [Tourille et al., 2018](http://www.aclweb.org/anthology/W18-5622).\n\n## Corpora\n\nThe different corpora are:\n+ [conll2003](https://github.com/strayMat/bio-medical_ner/tree/master/conll2003)\n+ [medpost](https://github.com/strayMat/bio-medical_ner/tree/master/medpost)\n+ [ncbi](https://github.com/strayMat/bio-medical_ner/tree/master/ncbi)\n\nEach of the folder contains a README.md, commented jupyter notebooks, a data folder and partial summary of the results in a json directory.  \n\n## Utils\n\nThe auxilliary functions used in notebooks are discribed in [utils_paper](https://github.com/strayMat/bio-medical_ner/tree/master/utils_paper).\n\n## Embeddings\n\nThe origin and construction of word embeddings used by the model are in [en_word_emb](https://github.com/strayMat/bio-medical_ner/tree/master/en_word_emb), a notebook describes how they are constructed.\n\n\n## Requirements:\n\nInstall the Python dependencies with :\n`pip install -r requirements.txt`\n\nInstall Yaset following [the instructions](http://yaset.readthedocs.io/en/stable/getting_started.html#installation)\n\n## Citation\n\nTourille, Julien, Matthieu Doutreligne, Olivier Ferret, Aurélie Névéol, Nicolas Paris, et Xavier Tannier. « Evaluation of a Sequence Tagging Tool for Biomedical Texts ». Proceedings of the 9th International Workshop on Health Text Mining and Information Analysis (LOUHI 2018), 2018, pages 193–203.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstraymat%2Fbio-medical_ner","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fstraymat%2Fbio-medical_ner","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fstraymat%2Fbio-medical_ner/lists"}