{"id":20837775,"url":"https://github.com/astrazeneca/gim","last_synced_at":"2026-04-13T02:41:27.251Z","repository":{"id":40954864,"uuid":"400442210","full_name":"AstraZeneca/GIM","owner":"AstraZeneca","description":"gene interaction matrices, a novel approach to using ConvNets on gene expression data","archived":false,"fork":false,"pushed_at":"2022-06-22T04:41:08.000Z","size":98,"stargazers_count":1,"open_issues_count":1,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-18T23:00:07.348Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Jupyter Notebook","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/AstraZeneca.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-08-27T08:31:26.000Z","updated_at":"2024-10-06T23:44:11.000Z","dependencies_parsed_at":"2022-09-04T01:02:21.805Z","dependency_job_id":null,"html_url":"https://github.com/AstraZeneca/GIM","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/AstraZeneca%2FGIM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2FGIM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2FGIM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/AstraZeneca%2FGIM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/AstraZeneca","download_url":"https://codeload.github.com/AstraZeneca/GIM/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243196243,"owners_count":20251849,"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":[],"created_at":"2024-11-18T01:08:32.927Z","updated_at":"2025-12-26T02:40:19.160Z","avatar_url":"https://github.com/AstraZeneca.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# GIM\r\n![Maturity level-0](https://img.shields.io/badge/Maturity%20Level-ML--0-red)\r\n\r\n# Introduction\r\nWe developed Gene Interaction Matrices (GIM) as a biologically inspired, gene-interaction based data transformation on gene expression data to create an image-like feature matrix from any gene expression-based study. The transformed data can then be used with any CNN based machine learning approaches for a variety of challenging problems such as disease diagnostics and drug development.\r\n\r\n# Dependencies\r\n```\r\npython \u003e= 3.7\r\nnumpy 1.20.3\r\npandas 1.3.0\r\n```\r\n\r\n# Usage\r\nAn example workflow to create a GIM is described here. To begin import the necessary dependencies and gim .py file containing the transform function.\r\n```\r\nimport pandas\r\nimport gim\r\n```\r\nLoad the treatment and control files containing one or more replicates from the gim/data/ directory.\r\n```\r\ndf_control_replicates = pd.read_csv(\"control_replicates.csv\")\r\ndf_treatment_replicates = pd.read_csv(\"treatment_replicates.csv\")\r\n```\r\nApply the gim_transform function to the files.\r\n```\r\nsample_img = gim.gim_transform(df_control_replicates, df_treatement_replicates)\r\n```\r\n\r\n# Reference\r\nPre-print: https://www.biorxiv.org/content/10.1101/2021.09.07.459284v1\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fastrazeneca%2Fgim","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fastrazeneca%2Fgim","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fastrazeneca%2Fgim/lists"}