{"id":26674378,"url":"https://github.com/multiomics-analytics-group/course_graph_machine_learning","last_synced_at":"2025-06-13T02:05:29.813Z","repository":{"id":271813987,"uuid":"914651337","full_name":"Multiomics-Analytics-Group/course_graph_machine_learning","owner":"Multiomics-Analytics-Group","description":"This is part of an AI course","archived":false,"fork":false,"pushed_at":"2025-01-13T15:12:35.000Z","size":14421,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-03-26T02:18:55.561Z","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":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Multiomics-Analytics-Group.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":"2025-01-10T02:57:05.000Z","updated_at":"2025-01-13T15:12:39.000Z","dependencies_parsed_at":"2025-01-10T03:27:56.085Z","dependency_job_id":"8ac65b13-02c2-48f0-a9bd-628c0162aa3b","html_url":"https://github.com/Multiomics-Analytics-Group/course_graph_machine_learning","commit_stats":null,"previous_names":["multiomics-analytics-group/course_graph_machine_learning"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Multiomics-Analytics-Group/course_graph_machine_learning","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2Fcourse_graph_machine_learning","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2Fcourse_graph_machine_learning/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2Fcourse_graph_machine_learning/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2Fcourse_graph_machine_learning/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Multiomics-Analytics-Group","download_url":"https://codeload.github.com/Multiomics-Analytics-Group/course_graph_machine_learning/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Multiomics-Analytics-Group%2Fcourse_graph_machine_learning/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259565566,"owners_count":22877347,"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":"2025-03-26T02:19:00.483Z","updated_at":"2025-06-13T02:05:29.788Z","avatar_url":"https://github.com/Multiomics-Analytics-Group.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Course 27666 AI-guided Protein Science\n\n# Graph Machine Learning\n\n## Course Structure\n\n| **Topics**   |                  Description       |         Hands-on            |Models           |\n|--------------|-------------------------|------------------------------|-----------------|\n|[Graphs](slides/Graphs.pdf)| Introduction to Graph Biology |  [**Data to Graphs**](notebooks/data2graphs.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Multiomics-Analytics-Group/course_graph_machine_learning/blob/main/notebooks/data2graphs.ipynb)     |                 |\n| [Graph Machine Learning](slides/GraphMachineLearning.pdf) |  An overview of the Graph Machine Learnign tasks and methods | 1. [**Intro to PyG**](notebooks/PyG_Introduction.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Multiomics-Analytics-Group/course_graph_machine_learning/blob/main/notebooks/PyG_Introduction.ipynb)  / 2. [**Shallow Embeddings**](notebooks/shallow_embeddings.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Multiomics-Analytics-Group/course_graph_machine_learning/blob/main/notebooks/shallow_embeddings.ipynb) | [Node2Vec](https://arxiv.org/abs/1607.00653) / [DeepWalk](https://arxiv.org/abs/1403.6652)  |\n| [Graph Neural Networks](slides/GraphNeuralNetworks.pdf) | Key concepts in GNNs |1. [**GNN Prediction**](notebooks/GNN_prediction.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Multiomics-Analytics-Group/course_graph_machine_learning/blob/main/notebooks/GNN_prediction.ipynb) / 2. [**Graph-level Prediction**](notebooks/graph_level_prediction.ipynb) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/Multiomics-Analytics-Group/course_graph_machine_learning/blob/main/notebooks/graph_level_prediction.ipynb) | [GNN](https://pytorch-geometric.readthedocs.io/en/2.6.1/cheatsheet/gnn_cheatsheet.html) |\n\n\n## Relevant links\n[IvLabs](https://ivlabs.github.io/resources/graph-representation-learning/)\n\n[Geometric Deep Learning](https://geometricdeeplearning.com/lectures/)\n\n[GNNs](https://github.com/SeongokRyu/Graph-neural-networks)\n\n[Stanford cs 224w](https://medium.com/stanford-cs224w)\n\n[Link prediction on Heterogeneous graphs](https://medium.com/@pytorch_geometric/link-prediction-on-heterogeneous-graphs-with-pyg-6d5c29677c70)\n\n[MLNTeam-Unical](https://mlnteam-unical.github.io/resources/)\n\n[Computational Network Biology](https://compnetbiocourse.discovery.wisc.edu/)\n\n[Combining Embeddings](https://medium.com/mantisnlp/how-to-combine-several-embeddings-models-8e7bc9a00330)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultiomics-analytics-group%2Fcourse_graph_machine_learning","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmultiomics-analytics-group%2Fcourse_graph_machine_learning","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmultiomics-analytics-group%2Fcourse_graph_machine_learning/lists"}