{"id":43499282,"url":"https://github.com/xomicsdatascience/geneformer","last_synced_at":"2026-02-03T11:13:20.238Z","repository":{"id":279303198,"uuid":"891114339","full_name":"xomicsdatascience/geneformer","owner":"xomicsdatascience","description":"A recreation of the geneformer model using AttentionSmithy","archived":false,"fork":false,"pushed_at":"2025-05-03T00:24:56.000Z","size":64,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-05-03T00:28:03.600Z","etag":null,"topics":[],"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/xomicsdatascience.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":"2024-11-19T18:49:05.000Z","updated_at":"2025-03-15T21:55:00.000Z","dependencies_parsed_at":"2025-02-24T22:25:11.736Z","dependency_job_id":"c08e5ff1-5448-43e1-b224-decf9f1b7f26","html_url":"https://github.com/xomicsdatascience/geneformer","commit_stats":null,"previous_names":["xomicsdatascience/geneformer"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/xomicsdatascience/geneformer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Fgeneformer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Fgeneformer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Fgeneformer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Fgeneformer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/xomicsdatascience","download_url":"https://codeload.github.com/xomicsdatascience/geneformer/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/xomicsdatascience%2Fgeneformer/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29044101,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-03T10:09:22.136Z","status":"ssl_error","status_checked_at":"2026-02-03T10:09:16.814Z","response_time":96,"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":"2026-02-03T11:13:19.542Z","updated_at":"2026-02-03T11:13:20.229Z","avatar_url":"https://github.com/xomicsdatascience.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# geneformer\nA recreation of the [Geneformer model described by Theodoris et al.](https://doi.org/10.1038/s41586-023-06139-9) using [AttentionSmithy](https://github.com/xomicsdatascience/AttentionSmithy).\n\n# Main Files\n## scripts/1_train_model.py\nThis file is the pre-training script for the geneformer foundation model.\n\n## scripts/2_fine_tune_model.py\nThis file is a training script for fine-tuning a pretrained geneformer model for a cell classification task.\n\n## src/geneformer/Geneformer.py\nThe code for the (pre-trained) geneformer foundation model. It was written using pytorch lightning for readability, and thus outlines the construction of the model, the forward pass process, and how that looks for training and validation steps.\n\n## src/geneformer/data/GeneformerDataModule.py\nThe code for preparing the data module used in training and validating the geneformer foundation model. It is made to be used with the pytorch lightning Trainer class, as called in model training scripts.\n\n## src/geneformer/fine_tuned_model/GeneformerForSequenceClassification.py\nThe code for the fine-tuned geneformer model. It was also written using pytorch lightning.\n\n## src/geneformer/fine_tuned_model/GeneformerDataModuleForSequenceClassification.py\nThe code for preparing the data module used in training and validating the fine-tuned geneformer model.\n\n# Citations, links\nTheodoris, C.V., Xiao, L., Chopra, A. et al. Transfer learning enables predictions in network biology. Nature 618, 616–624 (2023). https://doi.org/10.1038/s41586-023-06139-9\n\nhttps://huggingface.co/ctheodoris/Geneformer\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxomicsdatascience%2Fgeneformer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fxomicsdatascience%2Fgeneformer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fxomicsdatascience%2Fgeneformer/lists"}