{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:RG7TJU7GCZC7MKZED3B2GGEO7U","short_pith_number":"pith:RG7TJU7G","canonical_record":{"source":{"id":"2502.06126","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-10T03:25:14Z","cross_cats_sorted":[],"title_canon_sha256":"67e6c1587de5a9cc4ded7b84a235b7f227f9e4e25aef9a03bbc0730ce308d385","abstract_canon_sha256":"e955e89f8024d387300cd9fd3983e74c3dc8bce3004707db806fa77439b63def"},"schema_version":"1.0"},"canonical_sha256":"89bf34d3e61645f62b241ec3a3188efd0ae1f040fa2783d830cd0dbaa49d5eb7","source":{"kind":"arxiv","id":"2502.06126","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.06126","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"arxiv_version","alias_value":"2502.06126v1","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.06126","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"pith_short_12","alias_value":"RG7TJU7GCZC7","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"pith_short_16","alias_value":"RG7TJU7GCZC7MKZE","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"pith_short_8","alias_value":"RG7TJU7G","created_at":"2026-07-05T10:11:48Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:RG7TJU7GCZC7MKZED3B2GGEO7U","target":"record","payload":{"canonical_record":{"source":{"id":"2502.06126","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-10T03:25:14Z","cross_cats_sorted":[],"title_canon_sha256":"67e6c1587de5a9cc4ded7b84a235b7f227f9e4e25aef9a03bbc0730ce308d385","abstract_canon_sha256":"e955e89f8024d387300cd9fd3983e74c3dc8bce3004707db806fa77439b63def"},"schema_version":"1.0"},"canonical_sha256":"89bf34d3e61645f62b241ec3a3188efd0ae1f040fa2783d830cd0dbaa49d5eb7","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:11:48.185485Z","signature_b64":"04NdHksSgO7mcedxzYhYGi6etI0adFxhVBSul9Ckj10w8EcwKMW3Nkr/zRkg6gM2gHRORee4Jpslypjz2VBgDw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"89bf34d3e61645f62b241ec3a3188efd0ae1f040fa2783d830cd0dbaa49d5eb7","last_reissued_at":"2026-07-05T10:11:48.185001Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:11:48.185001Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2502.06126","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":"2026-07-05T10:11:48Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ACeMWCGlS2zAxLZ44MzEE0439uQqQAmggryJ7gAEAVj+7rSetUEj/93yKv1bpL90VOi5boDI7zlLYver0RWhCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-09T17:53:06.438565Z"},"content_sha256":"3728d763d5be075758cb56b46f7754f961c28067faa6bd4b5d5f63e4879b245b","schema_version":"1.0","event_id":"sha256:3728d763d5be075758cb56b46f7754f961c28067faa6bd4b5d5f63e4879b245b"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:RG7TJU7GCZC7MKZED3B2GGEO7U","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.LG","authors_text":"Dai Shi, Dmytro Matsypura, Junbin Gao, Kuan Yan, Lequan Lin, Ling Zhu, Mark C. Gillies, Ting Zhang, Yue Zeng","submitted_at":"2025-02-10T03:25:14Z","abstract_excerpt":"Understanding disease progression at the molecular pathway level usually requires capturing both structural dependencies between pathways and the temporal dynamics of disease evolution. In this work, we solve the former challenge by developing a biologically informed graph-forming method to efficiently construct pathway graphs for subjects from our newly curated JR5558 mouse transcriptomics dataset. We then develop Graph-level Pseudotime Analysis (GPA) to infer graph-level trajectories that reveal how disease progresses at the population level, rather than in individual subjects. Based on the "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.06126","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/2502.06126/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":"2026-07-05T10:11:48Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"DQTukhN/PRMEYZcGVkAII4Z93+TrQHdAcKysDs8b0dvK8xFutitobsj3im8hUehG8FF0Bq8YySnCavLc8kPmCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-09T17:53:06.439533Z"},"content_sha256":"b87baf9aedd64ae11d477207d6fa9f861c428f0b33f73104d697df2834448fe8","schema_version":"1.0","event_id":"sha256:b87baf9aedd64ae11d477207d6fa9f861c428f0b33f73104d697df2834448fe8"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/RG7TJU7GCZC7MKZED3B2GGEO7U/bundle.json","state_url":"https://pith.science/pith/RG7TJU7GCZC7MKZED3B2GGEO7U/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/RG7TJU7GCZC7MKZED3B2GGEO7U/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":"2026-08-09T17:53:06Z","links":{"resolver":"https://pith.science/pith/RG7TJU7GCZC7MKZED3B2GGEO7U","bundle":"https://pith.science/pith/RG7TJU7GCZC7MKZED3B2GGEO7U/bundle.json","state":"https://pith.science/pith/RG7TJU7GCZC7MKZED3B2GGEO7U/state.json","well_known_bundle":"https://pith.science/.well-known/pith/RG7TJU7GCZC7MKZED3B2GGEO7U/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:RG7TJU7GCZC7MKZED3B2GGEO7U","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":"e955e89f8024d387300cd9fd3983e74c3dc8bce3004707db806fa77439b63def","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-10T03:25:14Z","title_canon_sha256":"67e6c1587de5a9cc4ded7b84a235b7f227f9e4e25aef9a03bbc0730ce308d385"},"schema_version":"1.0","source":{"id":"2502.06126","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.06126","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"arxiv_version","alias_value":"2502.06126v1","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.06126","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"pith_short_12","alias_value":"RG7TJU7GCZC7","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"pith_short_16","alias_value":"RG7TJU7GCZC7MKZE","created_at":"2026-07-05T10:11:48Z"},{"alias_kind":"pith_short_8","alias_value":"RG7TJU7G","created_at":"2026-07-05T10:11:48Z"}],"graph_snapshots":[{"event_id":"sha256:b87baf9aedd64ae11d477207d6fa9f861c428f0b33f73104d697df2834448fe8","target":"graph","created_at":"2026-07-05T10:11:48Z","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/2502.06126/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Understanding disease progression at the molecular pathway level usually requires capturing both structural dependencies between pathways and the temporal dynamics of disease evolution. In this work, we solve the former challenge by developing a biologically informed graph-forming method to efficiently construct pathway graphs for subjects from our newly curated JR5558 mouse transcriptomics dataset. We then develop Graph-level Pseudotime Analysis (GPA) to infer graph-level trajectories that reveal how disease progresses at the population level, rather than in individual subjects. Based on the ","authors_text":"Dai Shi, Dmytro Matsypura, Junbin Gao, Kuan Yan, Lequan Lin, Ling Zhu, Mark C. Gillies, Ting Zhang, Yue Zeng","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-10T03:25:14Z","title":"Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.06126","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":"sha256:3728d763d5be075758cb56b46f7754f961c28067faa6bd4b5d5f63e4879b245b","target":"record","created_at":"2026-07-05T10:11:48Z","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":"e955e89f8024d387300cd9fd3983e74c3dc8bce3004707db806fa77439b63def","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-10T03:25:14Z","title_canon_sha256":"67e6c1587de5a9cc4ded7b84a235b7f227f9e4e25aef9a03bbc0730ce308d385"},"schema_version":"1.0","source":{"id":"2502.06126","kind":"arxiv","version":1}},"canonical_sha256":"89bf34d3e61645f62b241ec3a3188efd0ae1f040fa2783d830cd0dbaa49d5eb7","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"89bf34d3e61645f62b241ec3a3188efd0ae1f040fa2783d830cd0dbaa49d5eb7","first_computed_at":"2026-07-05T10:11:48.185001Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:11:48.185001Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"04NdHksSgO7mcedxzYhYGi6etI0adFxhVBSul9Ckj10w8EcwKMW3Nkr/zRkg6gM2gHRORee4Jpslypjz2VBgDw==","signature_status":"signed_v1","signed_at":"2026-07-05T10:11:48.185485Z","signed_message":"canonical_sha256_bytes"},"source_id":"2502.06126","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:3728d763d5be075758cb56b46f7754f961c28067faa6bd4b5d5f63e4879b245b","sha256:b87baf9aedd64ae11d477207d6fa9f861c428f0b33f73104d697df2834448fe8"],"state_sha256":"947c1f03be919baa08eb108b18381e72cad8722432b6f32849838902a881092b"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"OkoJQOTiZoWFVOGuSljc2wnKQBV9hVQ2TJSSXxh51Cxrqq80IdkCg7D6aWgBYQ/mhIzfv4wSkodtK1WrHJAECA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-09T17:53:06.447239Z","bundle_sha256":"4a808daee9420e8104363ad42a36b08425fda3927079303667e53648ac05fa59"}}