{"id":15601119,"url":"https://github.com/lucidrains/chroma-pytorch","last_synced_at":"2025-08-22T06:32:44.984Z","repository":{"id":64254794,"uuid":"573238843","full_name":"lucidrains/chroma-pytorch","owner":"lucidrains","description":"Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch","archived":false,"fork":false,"pushed_at":"2022-12-27T19:25:56.000Z","size":5207,"stargazers_count":158,"open_issues_count":3,"forks_count":23,"subscribers_count":19,"default_branch":"main","last_synced_at":"2024-12-10T16:50:26.947Z","etag":null,"topics":["artificial-intelligence","deep-learning","denoising-diffusion","graph-neural-networks","protein-design"],"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/lucidrains.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}},"created_at":"2022-12-02T01:57:50.000Z","updated_at":"2024-07-30T13:59:09.000Z","dependencies_parsed_at":"2023-01-15T07:00:32.905Z","dependency_job_id":null,"html_url":"https://github.com/lucidrains/chroma-pytorch","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucidrains%2Fchroma-pytorch","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucidrains%2Fchroma-pytorch/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucidrains%2Fchroma-pytorch/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lucidrains%2Fchroma-pytorch/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lucidrains","download_url":"https://codeload.github.com/lucidrains/chroma-pytorch/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":230568590,"owners_count":18246378,"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":["artificial-intelligence","deep-learning","denoising-diffusion","graph-neural-networks","protein-design"],"created_at":"2024-10-03T02:15:04.365Z","updated_at":"2024-12-20T10:08:29.296Z","avatar_url":"https://github.com/lucidrains.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003cimg src=\"./chroma.png\" width=\"550px\"\u003e\u003c/img\u003e\n\n\u003ci\u003efigure 1 in \u003ca href=\"https://www.biorxiv.org/content/10.1101/2022.12.01.518682v1\"\u003epaper\u003c/a\u003e\u003c/i\u003e\n\n\u003cimg src=\"./rfdiffusion.gif\" width=\"450px\"\u003e\u003c/img\u003e\n\n*generating a protein that binds to spike protein of coronavirus - Baker lab's concurrent RFDiffusion work*\n\n## Chroma - Pytorch (wip)\n\nImplementation of \u003ca href=\"https://generatebiomedicines.com/chroma\"\u003eChroma\u003c/a\u003e, generative model of proteins using DDPM and GNNs, in Pytorch. \u003ca href=\"https://www.bakerlab.org/2022/11/30/diffusion-model-for-protein-design/\"\u003eConcurrent work\u003c/a\u003e seems to suggest we have a slight lift-off applying denoising diffusion probabilistic models to protein design. Will also incorporate \u003ca href=\"https://arxiv.org/abs/2208.04202\"\u003eself-conditioning\u003c/a\u003e, applied successfully by Baker lab in RFDiffusion.\n\n\u003ca href=\"https://stephanheijl.com/rfdiffusion.html\"\u003eExplanation by Stephan Heijl\u003c/a\u003e\n\nIf you are interested in open sourcing works like these out in the wild, please consider joining \u003ca href=\"https://openbioml.org/\"\u003eOpenBioML\u003c/a\u003e\n\n## Todo\n\n- [ ] use \u003ca href=\"https://huggingface.co/mrm8488/galactica-125m\"\u003egalactica\u003c/a\u003e\n\n## Citations\n\n```bibtex\n@misc{\n    title   = {Illuminating protein space with a programmable generative model},\n    author  = {John Ingraham, Max Baranov, Zak Costello, Vincent Frappier, Ahmed Ismail, Shan Tie, Wujie Wang, Vincent Xue, Fritz Obermeyer, Andrew Beam, Gevorg Grigoryan},    \n    year    = {2022},\n    url     = {https://cdn.generatebiomedicines.com/assets/ingraham2022.pdf}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucidrains%2Fchroma-pytorch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flucidrains%2Fchroma-pytorch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flucidrains%2Fchroma-pytorch/lists"}