{"id":21280609,"url":"https://github.com/borgwardtlab/s3m","last_synced_at":"2025-07-11T10:32:28.225Z","repository":{"id":69455293,"uuid":"123930573","full_name":"BorgwardtLab/S3M","owner":"BorgwardtLab","description":"A software package for statistically significant shapelet mining","archived":false,"fork":false,"pushed_at":"2022-12-02T15:24:32.000Z","size":3020,"stargazers_count":52,"open_issues_count":0,"forks_count":8,"subscribers_count":6,"default_branch":"master","last_synced_at":"2023-10-20T18:23:27.011Z","etag":null,"topics":["biomedical","biomedical-data-science","shapelets","significant-pattern-mining","time-series","time-series-analysis","time-series-analysis-tool"],"latest_commit_sha":null,"homepage":null,"language":"C++","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/BorgwardtLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-03-05T14:22:17.000Z","updated_at":"2023-08-06T15:41:05.000Z","dependencies_parsed_at":"2023-03-11T06:07:09.531Z","dependency_job_id":null,"html_url":"https://github.com/BorgwardtLab/S3M","commit_stats":null,"previous_names":[],"tags_count":1,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FS3M","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FS3M/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FS3M/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/BorgwardtLab%2FS3M/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/BorgwardtLab","download_url":"https://codeload.github.com/BorgwardtLab/S3M/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":225715546,"owners_count":17512903,"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":["biomedical","biomedical-data-science","shapelets","significant-pattern-mining","time-series","time-series-analysis","time-series-analysis-tool"],"created_at":"2024-11-21T10:37:19.993Z","updated_at":"2024-11-21T10:37:20.518Z","avatar_url":"https://github.com/BorgwardtLab.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"![](./data/s3m_logo.png)\n# S3M \u0026mdash; Statistically Significant Shapelet Mining\n\nThis is the implementation of the method described in the ISMB 2018\npaper [\u0026ldquo;Association mapping in biomedical time series via\nstatistically significant shapelet\nmining\u0026rdquo;](https://doi.org/10.1093/bioinformatics/bty246).\n\n[![Build Status](https://travis-ci.com/BorgwardtLab/S3M.svg?token=6PepXoG2x1QhsqBnBzHF\u0026branch=master)](https://travis-ci.com/BorgwardtLab/S3M)\n\n# Installation\n\nFor Mac OS X, we recommend installing S3M using the [`Homebrew` package\nmanager](https://brew.sh):\n\n    $ brew install BorgwardtLab/mlcb/s3m\n\nFor Debian and Ubuntu, please use the `.deb` file of the [latest release](https://github.com/BorgwardtLab/S3M/releases/latest)  and install it using:\n\n    $ sudo apt install s3m-latest.deb\n\nFor Arch Linux, please install S3M from [AUR](https://aur.archlinux.org/packages/s3m-git)\nusing [`pacaur`](https://github.com/rmarquis/pacaur) or\n[`trizen`](https://github.com/trizen/trizen), for example:\n\n    $ pacaur -S s3m\n    $ trizen -S s3m\n\nPlease refer to the [advanced build instructions](docs/advanced_build.md)\nfor more advanced build processes, including source builds and Docker\ninstallations.\n\n# Example\n\nWe provide a synthetic data set that illustrates the utility of S3M.\nAfter installation, the command\n\n    $ s3m -i data/example/synthetic.csv -m 15 -o results/example.json\n\nruns S3M on it and stores its results in the `results` folder. The below\nfigure shows how the method identifies the case-characteristic two\nspikes as the most significant shapelet\u0026nbsp;(p-value: 5.42e-20).\n\n![](./results/example.png)\n\n# Help\n\nIf you have questions concerning S3M or you encounter problems when\ntrying to build the tool under your own system, please open an issue in\n[the issue tracker](https://github.com/BorgwardtLab/S3M/issues). Try to\ndescribe the issue in sufficient detail in order to make it possible for\nus to help you.\n\n# Contributors\n\nS3M is developed and maintained by members of the [Machine Learning and\nComputational Biology Lab](https://www.bsse.ethz.ch/mlcb) of [Prof. Dr.\nKarsten Borgwardt](https://www.bsse.ethz.ch/mlcb/karsten.html):\n\n- Christian Bock ([GitHub](https://github.com/chrisby))\n- Thomas Gumbsch ([GitHub](https://github.com/tgumbsch))\n- Max Horn ([GitHub](https://github.com/maexlich))\n- Michael Moor ([GitHub](https://github.com/mi92))\n- Bastian Rieck ([GitHub](https://github.com/Submanifold))\n\n# Citation\n\nPlease use the following BibTeX citation when using our method or\ncomparing against it:\n\n```TeX\n@article{Bock18,\n  author  = {Bock, Christian and Gumbsch, Thomas and Moor, Michael and Rieck, Bastian and Roqueiro, Damian and Borgwardt, Karsten},\n  title   = {Association mapping in biomedical time series via statistically significant shapelet mining},\n  journal = {Bioinformatics},\n  volume  = {34},\n  number  = {13},\n  pages   = {i438--i446},\n  year    = {2018},\n  doi     = {10.1093/bioinformatics/bty246},\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fs3m","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fborgwardtlab%2Fs3m","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fborgwardtlab%2Fs3m/lists"}