{"id":13481325,"url":"https://github.com/pfnet-research/hierarchical-molecular-learning","last_synced_at":"2025-04-13T10:27:08.169Z","repository":{"id":86583147,"uuid":"138020129","full_name":"pfnet-research/hierarchical-molecular-learning","owner":"pfnet-research","description":"Implementation of \"Semi-supervised learning of hierarchical representations of molecules using neural message passing\" (arXiv:1711.10168)","archived":false,"fork":false,"pushed_at":"2018-06-20T11:01:26.000Z","size":55,"stargazers_count":14,"open_issues_count":0,"forks_count":6,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-03-27T01:51:26.362Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/pfnet-research.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":"2018-06-20T10:56:20.000Z","updated_at":"2024-01-01T21:30:58.000Z","dependencies_parsed_at":null,"dependency_job_id":"4850f91a-8059-46ea-98b8-8ec2c8a7c560","html_url":"https://github.com/pfnet-research/hierarchical-molecular-learning","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/pfnet-research%2Fhierarchical-molecular-learning","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2Fhierarchical-molecular-learning/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2Fhierarchical-molecular-learning/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pfnet-research%2Fhierarchical-molecular-learning/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pfnet-research","download_url":"https://codeload.github.com/pfnet-research/hierarchical-molecular-learning/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248697392,"owners_count":21147320,"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":"2024-07-31T17:00:50.873Z","updated_at":"2025-04-13T10:27:08.143Z","avatar_url":"https://github.com/pfnet-research.png","language":"Python","funding_links":[],"categories":["Deep Learning"],"sub_categories":[],"readme":"This is implementation of [Semi-supervised learning of hierarchical representations of molecules using neural message passing](https://arxiv.org/abs/1711.10168) presetented at NIPS2017 [Workshop on Machine Learning for Molecules and Materials](http://www.quantum-machine.org/workshops/nips2017/).\n\n\n# Dependency\n\n* Chainer (\u003c=3.1.0)\n* NumPy\n* SciPy\n* scikit-learn\n* six\n\nYou can install these packages with pip by `pip install -r requirements.txt`\nor create a conda environment with these packages installed by `conda env create -n \u003cenv name\u003e --file env.yaml`.\n\nWe confirm the code with following environment.\n\n```\nchainer==3.1.0\nnumpy==1.13.3\nscikit-learn==0.19.1\nscipy==1.0.1\nsix==1.10.0\n```\n\nNote that this code does not work with Chainer newer than v3.1.0 due to changes made in Chainer.\nWe will solve the problem by fixing Chainer itself.\nSee [chainer/chainer#4877](https://github.com/chainer/chainer/issues/4877) for detail.\n\n\n# Usage\n\n```python\ncd unsupNFP\npython train.py mutag  # Use the MUTAG dataset\npython train.py ptc # Use the PTC dataset\n```\n\nThis repository has code for the experiments of unsupervised setting only.\nCode for the semi-supervised setting is under preparation.\n\n# Data source\n\n* MUTAG: [BorgwardtLab/GraphKernels](https://github.com/BorgwardtLab/GraphKernels)\n* PTC: [predictive-toxicology.org](https://www.predictive-toxicology.org)\n* malaria: [HIPS/neural-fingerprint](https://github.com/HIPS/neural-fingerprint)\n\n# Reference\n\nNguyen, H., Maeda, S. I., \u0026 Oono, K. (2017). Semi-supervised learning of hierarchical representations of molecules using neural message passing. arXiv preprint arXiv:1711.10168 [URL](https://arxiv.org/abs/1711.10168).\n\n\n# Contact\n\nKenta Oono (oono@preferred.jp)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpfnet-research%2Fhierarchical-molecular-learning","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpfnet-research%2Fhierarchical-molecular-learning","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpfnet-research%2Fhierarchical-molecular-learning/lists"}