{"id":37618481,"url":"https://github.com/jvrana/caldera","last_synced_at":"2026-01-16T10:35:08.563Z","repository":{"id":57457900,"uuid":"286892525","full_name":"jvrana/caldera","owner":"jvrana","description":"🌋 Pytorch extension for training on biological network data 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hash: .github/workflows/pre-commit.yml:20: update your workflow using https://app.stepsecurity.io/secureworkflow/jvrana/caldera/pre-commit.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/pre-commit.yml:25: update your workflow using https://app.stepsecurity.io/secureworkflow/jvrana/caldera/pre-commit.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:28: update your workflow using https://app.stepsecurity.io/secureworkflow/jvrana/caldera/tests.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/tests.yml:44: update your workflow using https://app.stepsecurity.io/secureworkflow/jvrana/caldera/tests.yml/master?enable=pin","Warn: containerImage not pinned by hash: docker/cpu/Dockerfile:1","Warn: containerImage not pinned by hash: docker/cpu/Dockerfile:7","Warn: containerImage not pinned by hash: docker/cpu/Dockerfile:10","Warn: containerImage not pinned by hash: docker/cpu/Dockerfile:13","Warn: containerImage not pinned by hash: docker/cpu/Dockerfile:18","Warn: containerImage not pinned by hash: docker/cpu/Dockerfile:22","Warn: containerImage not pinned by hash: docker/cu101/Dockerfile:1","Warn: containerImage not pinned by hash: docker/cu101/Dockerfile:6","Warn: containerImage not pinned by hash: docker/cu101/Dockerfile:10","Warn: containerImage not pinned by hash: docker/docs/Dockerfile:1","Warn: containerImage not pinned by hash: docker/docs/Dockerfile:7","Warn: containerImage not pinned by hash: docker/docs/Dockerfile:10","Warn: containerImage not pinned by hash: docker/docs/Dockerfile:13","Warn: containerImage not pinned by hash: docker/docs/Dockerfile:18","Warn: containerImage not pinned by hash: docker/docs/Dockerfile:22","Warn: containerImage not pinned by hash: docker/docs/Dockerfile:26","Warn: pipCommand not pinned by hash: docker/cpu/Dockerfile:4","Warn: pipCommand not pinned by hash: docker/cpu/Dockerfile:5","Warn: pipCommand not pinned by hash: docker/cpu/Dockerfile:8","Warn: pipCommand not pinned by hash: docker/cpu/Dockerfile:11","Warn: pipCommand not pinned by hash: docker/cpu/Dockerfile:16","Warn: pipCommand not pinned by hash: docker/cpu/Dockerfile:20","Warn: pipCommand not pinned by hash: docker/cpu/Dockerfile:24","Warn: pipCommand not pinned by hash: docker/cu101/Dockerfile:3","Warn: pipCommand not pinned by hash: docker/cu101/Dockerfile:4","Warn: pipCommand not pinned by hash: docker/cu101/Dockerfile:8","Warn: pipCommand not pinned by hash: docker/cu101/Dockerfile:13","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:4","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:5","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:8","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:11","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:16","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:20","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:24","Warn: pipCommand not pinned by hash: docker/docs/Dockerfile:28","Warn: pipCommand not pinned by hash: .github/workflows/pre-commit.yml:23","Warn: pipCommand not pinned by hash: .github/workflows/pre-commit.yml:24","Info:   0 out of   6 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   1 third-party GitHubAction dependencies pinned","Info:   0 out of  16 containerImage dependencies pinned","Info:   0 out of  21 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Vulnerabilities","score":0,"reason":"145 existing vulnerabilities detected","details":["Warn: Project is vulnerable to: PYSEC-2024-48 / GHSA-fj7x-q9j7-g6q6","Warn: Project is vulnerable to: PYSEC-2021-865 / GHSA-vv2x-vrpj-qqpq","Warn: Project is vulnerable to: PYSEC-2022-42986 / GHSA-43fp-rhv2-5gv8","Warn: Project is vulnerable to: PYSEC-2023-135 / GHSA-xqr8-7jwr-rhp7","Warn: Project is vulnerable to: GHSA-3ww4-gg4f-jr7f","Warn: Project is vulnerable to: GHSA-5cpq-8wj7-hf2v","Warn: Project is vulnerable to: GHSA-9v9h-cgj8-h64p","Warn: Project is vulnerable to: PYSEC-2021-62 / GHSA-hggm-jpg3-v476","Warn: Project is vulnerable to: GHSA-jm77-qphf-c4w8","Warn: Project is vulnerable to: GHSA-v8gr-m533-ghj9","Warn: Project is vulnerable to: GHSA-w7pp-m8wf-vj6r","Warn: Project is vulnerable to: GHSA-x4qr-2fvf-3mr5","Warn: Project is vulnerable to: PYSEC-2022-42991 / GHSA-v3c5-jqr6-7qm8","Warn: Project is vulnerable to: PYSEC-2024-4 / GHSA-2mqj-m65w-jghx","Warn: Project is vulnerable to: PYSEC-2023-165 / GHSA-cwvm-v4w8-q58c","Warn: Project is vulnerable to: PYSEC-2022-42992 / GHSA-hcpj-qp55-gfph","Warn: Project is vulnerable to: PYSEC-2023-137 / GHSA-pr76-5cm5-w9cj","Warn: Project is vulnerable to: PYSEC-2023-161 / GHSA-wfm5-v35h-vwf4","Warn: Project is vulnerable to: PYSEC-2024-60 / GHSA-jjg7-2v4v-x38h","Warn: Project is vulnerable to: GHSA-29gw-9793-fvw7","Warn: Project is vulnerable to: PYSEC-2022-12 / GHSA-pq7m-3gw7-gq5x","Warn: Project is vulnerable to: GHSA-cpwx-vrp4-4pq7","Warn: Project is vulnerable to: PYSEC-2021-66 / GHSA-g3rq-g295-4j3m","Warn: Project is vulnerable to: GHSA-h5c8-rqwp-cp95","Warn: Project is vulnerable to: GHSA-h75v-3vvj-5mfj","Warn: Project is vulnerable to: GHSA-q2x7-8rv6-6q7h","Warn: Project is vulnerable to: GHSA-33p9-3p43-82vq","Warn: Project is vulnerable to: PYSEC-2022-42974 / GHSA-m678-f26j-3hrp","Warn: Project is vulnerable to: GHSA-44cc-43rp-5947","Warn: Project is vulnerable to: PYSEC-2021-130 / GHSA-4952-p58q-6crx","Warn: Project is vulnerable to: GHSA-9q39-rmj3-p4r2","Warn: Project is vulnerable to: PYSEC-2022-249 / GHSA-9jmq-rx5f-8jwq","Warn: Project is vulnerable to: PYSEC-2020-215 / GHSA-c7vm-f5p4-8fqh","Warn: Project is vulnerable to: GHSA-hwvq-6gjx-j797","Warn: Project is vulnerable to: PYSEC-2022-180 / GHSA-m87f-39q9-6f55","Warn: Project is vulnerable to: PYSEC-2022-212 / GHSA-v7vq-3x77-87vg","Warn: Project is vulnerable to: GHSA-6p56-wp2h-9hxr","Warn: Project is vulnerable to: GHSA-fpfv-jqm9-f5jm","Warn: Project is vulnerable to: GHSA-3f63-hfp8-52jq","Warn: Project is vulnerable to: PYSEC-2021-41 / GHSA-3wvg-mj6g-m9cv","Warn: Project is vulnerable to: GHSA-44wm-f244-xhp3","Warn: Project is vulnerable to: GHSA-4fx9-vc88-q2xc","Warn: Project is vulnerable to: PYSEC-2021-35 / GHSA-57h3-9rgr-c24m","Warn: Project is vulnerable to: PYSEC-2021-331 / GHSA-7534-mm45-c74v","Warn: Project is vulnerable to: PYSEC-2021-137 / GHSA-77gc-v2xv-rvvh","Warn: Project is vulnerable to: PYSEC-2021-92 / GHSA-7r7m-5h27-29hp","Warn: Project is vulnerable to: PYSEC-2023-227 / GHSA-8ghj-p4vj-mr35","Warn: Project is vulnerable to: PYSEC-2022-10 / GHSA-8vj2-vxx3-667w","Warn: Project is vulnerable to: PYSEC-2021-36 / GHSA-8xjq-8fcg-g5hw","Warn: Project is vulnerable to: PYSEC-2021-42 / GHSA-95q3-8gr9-gm8w","Warn: Project is vulnerable to: PYSEC-2021-317 / GHSA-98vv-pw6r-q6q4","Warn: Project is vulnerable to: PYSEC-2021-38 / GHSA-9hx2-hgq2-2g4f","Warn: Project is vulnerable to: PYSEC-2022-168 / GHSA-9j59-75qj-795w","Warn: Project is vulnerable to: PYSEC-2021-40 / GHSA-f4w8-cv6p-x6r5","Warn: Project is vulnerable to: PYSEC-2021-69 / GHSA-f5g8-5qq7-938w","Warn: Project is vulnerable to: PYSEC-2021-139 / GHSA-g6rj-rv7j-xwp4","Warn: Project is vulnerable to: PYSEC-2021-71 / GHSA-hf64-x4gq-p99h","Warn: Project is vulnerable to: PYSEC-2021-94 / GHSA-hjfx-8p6c-g7gx","Warn: Project is vulnerable to: GHSA-j7hp-h8jx-5ppr","Warn: Project is vulnerable to: GHSA-jgpv-4h4c-xhw3","Warn: Project is vulnerable to: PYSEC-2022-42979 / GHSA-m2vv-5vj5-2hm7","Warn: Project is vulnerable to: PYSEC-2021-37 / GHSA-mvg9-xffr-p774","Warn: Project is vulnerable to: PYSEC-2021-39 / GHSA-p43w-g3c5-g5mq","Warn: Project is vulnerable to: PYSEC-2022-8 / GHSA-pw3c-h7wp-cvhx","Warn: Project is vulnerable to: PYSEC-2021-93 / GHSA-q5hq-fp76-qmrc","Warn: Project is vulnerable to: PYSEC-2021-138 / GHSA-rwv7-3v45-hg29","Warn: Project is vulnerable to: PYSEC-2021-70 / GHSA-vqcj-wrf2-7v73","Warn: Project is vulnerable to: PYSEC-2022-9 / GHSA-xrcv-f9gm-v42c","Warn: Project is vulnerable to: PYSEC-2023-175","Warn: Project is vulnerable to: PYSEC-2021-437 / GHSA-5xp3-jfq3-5q8x","Warn: Project is vulnerable to: PYSEC-2023-228 / GHSA-mq26-g339-26xf","Warn: Project is vulnerable to: PYSEC-2020-92 / GHSA-hj5v-574p-mj7c","Warn: Project is vulnerable to: PYSEC-2022-42969","Warn: Project is vulnerable to: PYSEC-2021-140 / GHSA-9w8r-397f-prfh","Warn: Project is vulnerable to: PYSEC-2023-117 / GHSA-mrwq-x4v8-fh7p","Warn: Project is vulnerable to: PYSEC-2021-141 / GHSA-pq64-v7f5-gqh8","Warn: Project is vulnerable to: PYSEC-2021-142 / GHSA-8q59-q68h-6hv4","Warn: Project is vulnerable to: GHSA-9hjg-9r4m-mvj7","Warn: Project is vulnerable to: GHSA-9wx4-h78v-vm56","Warn: Project is vulnerable to: PYSEC-2023-74 / GHSA-j8r2-6x86-q33q","Warn: Project is vulnerable to: PYSEC-2023-102","Warn: Project is vulnerable to: PYSEC-2023-114","Warn: Project is vulnerable to: GHSA-29pr-6jr8-q5jm","Warn: Project is vulnerable to: GHSA-g92j-qhmh-64v2","Warn: Project is vulnerable to: PYSEC-2025-49 / GHSA-5rjg-fvgr-3xxf","Warn: Project is vulnerable to: GHSA-cx63-2mw6-8hw5","Warn: Project is vulnerable to: PYSEC-2022-43012 / GHSA-r9hx-vwmv-q579","Warn: Project is vulnerable to: GHSA-3749-ghw9-m3mg","Warn: Project is vulnerable to: PYSEC-2022-43015 / GHSA-47fc-vmwq-366v","Warn: Project is vulnerable to: PYSEC-2025-41 / GHSA-53q9-r3pm-6pq6","Warn: Project is vulnerable to: PYSEC-2024-252 / GHSA-5pcm-hx3q-hm94","Warn: Project is vulnerable to: GHSA-887c-mr87-cxwp","Warn: Project is vulnerable to: PYSEC-2024-251 / GHSA-pg7h-5qx3-wjr3","Warn: Project is vulnerable to: PYSEC-2024-250","Warn: Project is vulnerable to: PYSEC-2024-259","Warn: Project is vulnerable to: GHSA-753j-mpmx-qq6g","Warn: Project is vulnerable to: GHSA-7cx3-6m66-7c5m","Warn: Project is vulnerable to: GHSA-8w49-h785-mj3c","Warn: Project is vulnerable to: PYSEC-2023-75 / GHSA-hj3f-6gcp-jg8j","Warn: Project is vulnerable to: GHSA-qppv-j76h-2rpx","Warn: Project is vulnerable to: GHSA-w235-7p84-xx57","Warn: Project is vulnerable to: GHSA-g7vv-2v7x-gj9p","Warn: Project is vulnerable to: GHSA-34jh-p97f-mpxf","Warn: Project is vulnerable to: PYSEC-2023-212 / GHSA-g4mx-q9vg-27p4","Warn: Project is vulnerable to: GHSA-pq67-6m6q-mj2v","Warn: Project is vulnerable to: PYSEC-2021-108 / GHSA-q2q7-5pp4-w6pg","Warn: Project is vulnerable to: PYSEC-2023-192 / GHSA-v845-jxx5-vc9f","Warn: Project is vulnerable to: PYSEC-2024-187 / GHSA-rqc4-2hc7-8c8v","Warn: Project is vulnerable to: PYSEC-2022-43017 / GHSA-qwmp-2cf2-g9g6","Warn: Project is vulnerable to: GHSA-jfmj-5v4g-7637","Warn: Project is vulnerable to: PYSEC-2023-120 / GHSA-45c4-8wx5-qw6w","Warn: Project is vulnerable to: PYSEC-2024-24 / GHSA-5h86-8mv2-jq9f","Warn: Project is vulnerable to: GHSA-5m98-qgg9-wh84","Warn: Project is vulnerable to: GHSA-7gpw-8wmc-pm8g","Warn: Project is vulnerable to: GHSA-8495-4g3g-x7pr","Warn: Project is vulnerable to: PYSEC-2024-26 / GHSA-8qpw-xqxj-h4r2","Warn: Project is vulnerable to: GHSA-9548-qrrj-x5pj","Warn: Project is vulnerable to: PYSEC-2023-246 / GHSA-gfw2-4jvh-wgfg","Warn: Project is vulnerable to: GHSA-pjjw-qhg8-p2p9","Warn: Project is vulnerable to: PYSEC-2023-250 / GHSA-q3qx-c6g2-7pw2","Warn: Project is vulnerable to: PYSEC-2023-251 / GHSA-qvrw-v9rv-5rjx","Warn: Project is vulnerable to: PYSEC-2021-76 / GHSA-v6wp-4m6f-gcjg","Warn: Project is vulnerable to: PYSEC-2023-247 / GHSA-xx9p-xxvh-7g8j","Warn: Project is vulnerable to: PYSEC-2021-421 / GHSA-h4m5-qpfp-3mpv","Warn: Project is vulnerable to: PYSEC-2022-43178 / GHSA-2p9h-ccw7-33gf","Warn: Project is vulnerable to: GHSA-496j-2rq6-j6cc","Warn: Project is vulnerable to: PYSEC-2022-266 / GHSA-9xgj-fcgf-x6mw","Warn: Project is vulnerable to: PYSEC-2022-43179 / GHSA-j4j9-7hg9-97g6","Warn: Project is vulnerable to: PYSEC-2022-234 / GHSA-xr2c-5w89-63pv","Warn: Project is vulnerable to: PYSEC-2022-48 / GHSA-77rm-9x9h-xj3g","Warn: Project is vulnerable to: GHSA-8gq9-2x98-w8hf","Warn: Project is vulnerable to: GHSA-8qvm-5x2c-j2w7","Warn: Project is vulnerable to: PYSEC-2021-874 / GHSA-2vj5-px25-gjrp","Warn: Project is vulnerable to: GHSA-4cv3-v7pv-rfhf","Warn: Project is vulnerable to: GHSA-98fp-7v67-4v3q","Warn: Project is vulnerable to: PYSEC-2022-181 / GHSA-r5qj-cvf9-p85h","Warn: Project is vulnerable to: PYSEC-2021-112 / GHSA-hwfp-hg2m-9vr2","Warn: Project is vulnerable to: PYSEC-2020-100 / GHSA-xrx6-fmxq-rjj2","Warn: Project is vulnerable to: GHSA-2g68-c3qc-8985","Warn: Project is vulnerable to: GHSA-f9vj-2wh5-fj8j","Warn: Project is vulnerable to: PYSEC-2023-221 / GHSA-hrfv-mqp8-q5rw","Warn: Project is vulnerable to: PYSEC-2023-57 / GHSA-px8h-6qxv-m22q","Warn: Project is vulnerable to: GHSA-q34m-jh98-gwm2","Warn: Project is vulnerable to: PYSEC-2023-58 / GHSA-xg9f-g7g7-2323","Warn: Project is vulnerable to: PYSEC-2022-203"],"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}}]},"last_synced_at":"2025-08-20T09:14:29.138Z","repository_id":57457900,"created_at":"2025-08-20T09:14:29.138Z","updated_at":"2025-08-20T09:14:29.138Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478050,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T06:30:42.265Z","status":"ssl_error","status_checked_at":"2026-01-16T06:30:16.248Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["causal","deep-learning","graph","network","pytorch"],"created_at":"2026-01-16T10:35:07.824Z","updated_at":"2026-01-16T10:35:08.555Z","avatar_url":"https://github.com/jvrana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Caldera 🌋\n\n![Code Quality](https://github.com/jvrana/caldera/workflows/Code%20Quality/badge.svg)\n![Tests](https://github.com/jvrana/caldera/workflows/Tests/badge.svg)\n![Documentation](https://github.com/jvrana/caldera/workflows/Documentation/badge.svg)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit\u0026logoColor=white)](https://github.com/pre-commit/pre-commit)\n\n**PLEASE NOTE PROJECT HAS MOVED TO [Caldera2](https://github.com/jvrana/Caldera2)**\n\n**Caldera** is a Pytorch extension for learning on graphical data. It learns underlying causal relationships in data.\n\n## Gallery\n\n## Usage\n\n### Installation\n\n#### via pip\n\n#### via Conda\n\n#### via Docker\n\n**Build CUDA enable image**\n\n```\ndocker build . -f docker/cu101/Dockerfile\n```\n\n**Build slim cpu-only image**\n\n```\ndocker build . -f docker/cpu/Dockerfile\n```\n\n### Tour\n\n## Acknowledgements\n\n* [rusty1s/pytorch_scatter](https://github.com/rusty1s/pytorch_scatter) - an awesome library that provides missing \nscatter methods in pytorch. Necessary for graph attribute aggregation\n* PyTorch Geometric - \n* PGN - provided a blueprint for implementing this library\n\n## References\n\n**Inspirations**\n\n* Pytorch Geometric [ADD REF]\n* GraphNets [ADD REF]\n* Pyro Probabilistic Programming Language\n* Pearl, J. (2009). Causality: Models, Reasoning and Inference.\n* Pearl, J. (2018). Theoretical impediments to machine learning with seven sparks from the causal revolution.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjvrana%2Fcaldera","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjvrana%2Fcaldera","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjvrana%2Fcaldera/lists"}