{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:SFQZ55T7I72L5N4AOZTX3KYTE5","short_pith_number":"pith:SFQZ55T7","canonical_record":{"source":{"id":"2409.05804","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2024-09-09T17:10:36Z","cross_cats_sorted":["q-bio.TO"],"title_canon_sha256":"47b699a5d8b9f1895a8a26fc8a1c0bd04221373493078ef39e967f9f448f966f","abstract_canon_sha256":"5f0c62cfe6b1856bb336a09a09b111b0ea37877f53ab7c250859e6459ebf5a02"},"schema_version":"1.0"},"canonical_sha256":"91619ef67f47f4beb78076677dab13274fdb35c55fb019f0cdc25d143c910cb2","source":{"kind":"arxiv","id":"2409.05804","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2409.05804","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"arxiv_version","alias_value":"2409.05804v1","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2409.05804","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"pith_short_12","alias_value":"SFQZ55T7I72L","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"pith_short_16","alias_value":"SFQZ55T7I72L5N4A","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"pith_short_8","alias_value":"SFQZ55T7","created_at":"2026-07-05T09:04:54Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:SFQZ55T7I72L5N4AOZTX3KYTE5","target":"record","payload":{"canonical_record":{"source":{"id":"2409.05804","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2024-09-09T17:10:36Z","cross_cats_sorted":["q-bio.TO"],"title_canon_sha256":"47b699a5d8b9f1895a8a26fc8a1c0bd04221373493078ef39e967f9f448f966f","abstract_canon_sha256":"5f0c62cfe6b1856bb336a09a09b111b0ea37877f53ab7c250859e6459ebf5a02"},"schema_version":"1.0"},"canonical_sha256":"91619ef67f47f4beb78076677dab13274fdb35c55fb019f0cdc25d143c910cb2","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T09:04:54.376955Z","signature_b64":"Bm+FF712xq0sdrhpDUE7q4974U35Ll6AYr9Ah5+yYr6hLyGZFfJYR/E3dBEwwotQFw7BHg1+HtMQi5U3iZDfAw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"91619ef67f47f4beb78076677dab13274fdb35c55fb019f0cdc25d143c910cb2","last_reissued_at":"2026-07-05T09:04:54.376542Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T09:04:54.376542Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2409.05804","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T09:04:54Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"HbBZ+HGdM3OatssHECeo2NWkAEzkJYE+yDPRnTUNgi/Zn6B7NEjbOfMlqxqRtEqMSgNgXvLX0FRNUcfLYr9ICQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-23T00:14:07.340944Z"},"content_sha256":"b5a482aa09c2f78189fca8530a472dad6272dad711ea1c03b2e496be2493618d","schema_version":"1.0","event_id":"sha256:b5a482aa09c2f78189fca8530a472dad6272dad711ea1c03b2e496be2493618d"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:SFQZ55T7I72L5N4AOZTX3KYTE5","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":["q-bio.TO"],"primary_cat":"cs.LG","authors_text":"Carola-Bibiane Schonlieb, Daniel G. Chen, Krzysztof Polanski, Moshe Eliasof, Sarah A. Teichmann, Stathis Megas","submitted_at":"2024-09-09T17:10:36Z","abstract_excerpt":"Celcomen leverages a mathematical causality framework to disentangle intra- and inter- cellular gene regulation programs in spatial transcriptomics and single-cell data through a generative graph neural network. It can learn gene-gene interactions, as well as generate post-perturbation counterfactual spatial transcriptomics, thereby offering access to experimentally inaccessible samples. We validated its disentanglement, identifiability, and counterfactual prediction capabilities through simulations and in clinically relevant human glioblastoma, human fetal spleen, and mouse lung cancer sample"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2409.05804","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2409.05804/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T09:04:54Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"6PRRQmF+g78tH9VWcQ6H+GwAqNbQhN9G+Gh61tLAXIEsPj+ZiHDZWNt5nqg33u8LHFOE4/lv/LnsHmS9m3yfAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-23T00:14:07.341441Z"},"content_sha256":"101d6185ae62f297cd4d497052a3680568246a0b1810d3e12068fd949b39d237","schema_version":"1.0","event_id":"sha256:101d6185ae62f297cd4d497052a3680568246a0b1810d3e12068fd949b39d237"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/SFQZ55T7I72L5N4AOZTX3KYTE5/bundle.json","state_url":"https://pith.science/pith/SFQZ55T7I72L5N4AOZTX3KYTE5/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/SFQZ55T7I72L5N4AOZTX3KYTE5/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-08-23T00:14:07Z","links":{"resolver":"https://pith.science/pith/SFQZ55T7I72L5N4AOZTX3KYTE5","bundle":"https://pith.science/pith/SFQZ55T7I72L5N4AOZTX3KYTE5/bundle.json","state":"https://pith.science/pith/SFQZ55T7I72L5N4AOZTX3KYTE5/state.json","well_known_bundle":"https://pith.science/.well-known/pith/SFQZ55T7I72L5N4AOZTX3KYTE5/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:SFQZ55T7I72L5N4AOZTX3KYTE5","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"5f0c62cfe6b1856bb336a09a09b111b0ea37877f53ab7c250859e6459ebf5a02","cross_cats_sorted":["q-bio.TO"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2024-09-09T17:10:36Z","title_canon_sha256":"47b699a5d8b9f1895a8a26fc8a1c0bd04221373493078ef39e967f9f448f966f"},"schema_version":"1.0","source":{"id":"2409.05804","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2409.05804","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"arxiv_version","alias_value":"2409.05804v1","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2409.05804","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"pith_short_12","alias_value":"SFQZ55T7I72L","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"pith_short_16","alias_value":"SFQZ55T7I72L5N4A","created_at":"2026-07-05T09:04:54Z"},{"alias_kind":"pith_short_8","alias_value":"SFQZ55T7","created_at":"2026-07-05T09:04:54Z"}],"graph_snapshots":[{"event_id":"sha256:101d6185ae62f297cd4d497052a3680568246a0b1810d3e12068fd949b39d237","target":"graph","created_at":"2026-07-05T09:04:54Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2409.05804/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Celcomen leverages a mathematical causality framework to disentangle intra- and inter- cellular gene regulation programs in spatial transcriptomics and single-cell data through a generative graph neural network. It can learn gene-gene interactions, as well as generate post-perturbation counterfactual spatial transcriptomics, thereby offering access to experimentally inaccessible samples. We validated its disentanglement, identifiability, and counterfactual prediction capabilities through simulations and in clinically relevant human glioblastoma, human fetal spleen, and mouse lung cancer sample","authors_text":"Carola-Bibiane Schonlieb, Daniel G. Chen, Krzysztof Polanski, Moshe Eliasof, Sarah A. Teichmann, Stathis Megas","cross_cats":["q-bio.TO"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2024-09-09T17:10:36Z","title":"Celcomen: spatial causal disentanglement for single-cell and tissue perturbation modeling"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2409.05804","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:b5a482aa09c2f78189fca8530a472dad6272dad711ea1c03b2e496be2493618d","target":"record","created_at":"2026-07-05T09:04:54Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"5f0c62cfe6b1856bb336a09a09b111b0ea37877f53ab7c250859e6459ebf5a02","cross_cats_sorted":["q-bio.TO"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"cs.LG","submitted_at":"2024-09-09T17:10:36Z","title_canon_sha256":"47b699a5d8b9f1895a8a26fc8a1c0bd04221373493078ef39e967f9f448f966f"},"schema_version":"1.0","source":{"id":"2409.05804","kind":"arxiv","version":1}},"canonical_sha256":"91619ef67f47f4beb78076677dab13274fdb35c55fb019f0cdc25d143c910cb2","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"91619ef67f47f4beb78076677dab13274fdb35c55fb019f0cdc25d143c910cb2","first_computed_at":"2026-07-05T09:04:54.376542Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T09:04:54.376542Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"Bm+FF712xq0sdrhpDUE7q4974U35Ll6AYr9Ah5+yYr6hLyGZFfJYR/E3dBEwwotQFw7BHg1+HtMQi5U3iZDfAw==","signature_status":"signed_v1","signed_at":"2026-07-05T09:04:54.376955Z","signed_message":"canonical_sha256_bytes"},"source_id":"2409.05804","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:b5a482aa09c2f78189fca8530a472dad6272dad711ea1c03b2e496be2493618d","sha256:101d6185ae62f297cd4d497052a3680568246a0b1810d3e12068fd949b39d237"],"state_sha256":"44999a875252f343ac522aab117df00b413c886c4a772c3f49985c6bc6a8b67c"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"X7pn+Fw9wtmq/VnDQ9XAe3ET9JAPiY3nP9ktPDFEbX2FHSHFixyVf7UP/tA/Qy7wQkerDRAbBRTpRNLzspQ/Ag==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-23T00:14:07.346441Z","bundle_sha256":"7c5cb6a88256613b56171a72719959341094692ee50b92448c49d33af52841b4"}}