{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:RGQRWD2HFWXOF3YRSV5S2KXRCQ","short_pith_number":"pith:RGQRWD2H","canonical_record":{"source":{"id":"2405.17032","kind":"arxiv","version":4},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2024-05-27T10:39:18Z","cross_cats_sorted":["math.PR","q-bio.PE","stat.AP"],"title_canon_sha256":"2e2219c5986bd14e291f7c366c39618d8f685a46863710baf833a3cdc18b0a62","abstract_canon_sha256":"26496ec27e4673496b3d30e77969f8ff5ba004b48bc90ab0c1683a7e81ef9aa0"},"schema_version":"1.0"},"canonical_sha256":"89a11b0f472daee2ef11957b2d2af11407b81b7671a8a590deb7cc8374abde0e","source":{"kind":"arxiv","id":"2405.17032","version":4},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2405.17032","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"arxiv_version","alias_value":"2405.17032v4","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2405.17032","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"pith_short_12","alias_value":"RGQRWD2HFWXO","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"pith_short_16","alias_value":"RGQRWD2HFWXOF3YR","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"pith_short_8","alias_value":"RGQRWD2H","created_at":"2026-05-22T01:03:13Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:RGQRWD2HFWXOF3YRSV5S2KXRCQ","target":"record","payload":{"canonical_record":{"source":{"id":"2405.17032","kind":"arxiv","version":4},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2024-05-27T10:39:18Z","cross_cats_sorted":["math.PR","q-bio.PE","stat.AP"],"title_canon_sha256":"2e2219c5986bd14e291f7c366c39618d8f685a46863710baf833a3cdc18b0a62","abstract_canon_sha256":"26496ec27e4673496b3d30e77969f8ff5ba004b48bc90ab0c1683a7e81ef9aa0"},"schema_version":"1.0"},"canonical_sha256":"89a11b0f472daee2ef11957b2d2af11407b81b7671a8a590deb7cc8374abde0e","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-22T01:03:13.812717Z","signature_b64":"8hAph+ghfwedfvbuD9Ej0rqQ5QzZGj4uxDESOz+/1zfmQtKptswUJJA7zEJOyxCFuJMcmC95jkpO1r4+PoumAw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"89a11b0f472daee2ef11957b2d2af11407b81b7671a8a590deb7cc8374abde0e","last_reissued_at":"2026-05-22T01:03:13.811773Z","signature_status":"signed_v1","first_computed_at":"2026-05-22T01:03:13.811773Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2405.17032","source_version":4,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-22T01:03:13Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"60APGRoO/TnJa2XQaSBLHwYbvy2cntFwQlFtYsEF27YtpJKqVxNfWMKxOZcKuZzmK3xusrMN09qL4XQHru7VCA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-03T21:45:55.579403Z"},"content_sha256":"0d4f3c94d344bcdf7ca18500c13bd211cf6830fbc3e32f369cbd69f86f928676","schema_version":"1.0","event_id":"sha256:0d4f3c94d344bcdf7ca18500c13bd211cf6830fbc3e32f369cbd69f86f928676"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:RGQRWD2HFWXOF3YRSV5S2KXRCQ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Exact phylodynamic likelihood via structured Markov genealogy processes","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["math.PR","q-bio.PE","stat.AP"],"primary_cat":"q-bio.QM","authors_text":"Aaron A. King, Edward L. Ionides, Qianying Lin","submitted_at":"2024-05-27T10:39:18Z","abstract_excerpt":"We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed genealogy in terms of a filter equation, the structure of which is completely determined by the population model. We show that existing phylodynamic methods based on the coalescent and linear birth-death processes are special cases. We derive some properties of filter equations and describe a class of algorithms that can be used to numerically solve them. Impor"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2405.17032","kind":"arxiv","version":4},"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/2405.17032/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":"2026-05-22T01:03:13Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"dQDAEQmsCniZwutZdRCVk6EgdF5d1J+If4VKdlevDz3KAnRvP0wA/eBUbSrwF5Dq3inIBpptZGJQaUhPmYSQDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-03T21:45:55.579797Z"},"content_sha256":"2df0a5c40d0f08fea72c42fac6afb0a054bd0b86ccb62fa0b8a797aac837b875","schema_version":"1.0","event_id":"sha256:2df0a5c40d0f08fea72c42fac6afb0a054bd0b86ccb62fa0b8a797aac837b875"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/RGQRWD2HFWXOF3YRSV5S2KXRCQ/bundle.json","state_url":"https://pith.science/pith/RGQRWD2HFWXOF3YRSV5S2KXRCQ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/RGQRWD2HFWXOF3YRSV5S2KXRCQ/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":"2026-06-03T21:45:55Z","links":{"resolver":"https://pith.science/pith/RGQRWD2HFWXOF3YRSV5S2KXRCQ","bundle":"https://pith.science/pith/RGQRWD2HFWXOF3YRSV5S2KXRCQ/bundle.json","state":"https://pith.science/pith/RGQRWD2HFWXOF3YRSV5S2KXRCQ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/RGQRWD2HFWXOF3YRSV5S2KXRCQ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:RGQRWD2HFWXOF3YRSV5S2KXRCQ","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":"26496ec27e4673496b3d30e77969f8ff5ba004b48bc90ab0c1683a7e81ef9aa0","cross_cats_sorted":["math.PR","q-bio.PE","stat.AP"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2024-05-27T10:39:18Z","title_canon_sha256":"2e2219c5986bd14e291f7c366c39618d8f685a46863710baf833a3cdc18b0a62"},"schema_version":"1.0","source":{"id":"2405.17032","kind":"arxiv","version":4}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2405.17032","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"arxiv_version","alias_value":"2405.17032v4","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2405.17032","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"pith_short_12","alias_value":"RGQRWD2HFWXO","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"pith_short_16","alias_value":"RGQRWD2HFWXOF3YR","created_at":"2026-05-22T01:03:13Z"},{"alias_kind":"pith_short_8","alias_value":"RGQRWD2H","created_at":"2026-05-22T01:03:13Z"}],"graph_snapshots":[{"event_id":"sha256:2df0a5c40d0f08fea72c42fac6afb0a054bd0b86ccb62fa0b8a797aac837b875","target":"graph","created_at":"2026-05-22T01:03:13Z","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/2405.17032/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"We show that each member of a broad class of Markovian population models induces a unique stochastic process on the space of genealogies. We construct this genealogy process and derive exact expressions for the likelihood of an observed genealogy in terms of a filter equation, the structure of which is completely determined by the population model. We show that existing phylodynamic methods based on the coalescent and linear birth-death processes are special cases. We derive some properties of filter equations and describe a class of algorithms that can be used to numerically solve them. Impor","authors_text":"Aaron A. King, Edward L. Ionides, Qianying Lin","cross_cats":["math.PR","q-bio.PE","stat.AP"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2024-05-27T10:39:18Z","title":"Exact phylodynamic likelihood via structured Markov genealogy processes"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2405.17032","kind":"arxiv","version":4},"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":"sha256:0d4f3c94d344bcdf7ca18500c13bd211cf6830fbc3e32f369cbd69f86f928676","target":"record","created_at":"2026-05-22T01:03:13Z","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":"26496ec27e4673496b3d30e77969f8ff5ba004b48bc90ab0c1683a7e81ef9aa0","cross_cats_sorted":["math.PR","q-bio.PE","stat.AP"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2024-05-27T10:39:18Z","title_canon_sha256":"2e2219c5986bd14e291f7c366c39618d8f685a46863710baf833a3cdc18b0a62"},"schema_version":"1.0","source":{"id":"2405.17032","kind":"arxiv","version":4}},"canonical_sha256":"89a11b0f472daee2ef11957b2d2af11407b81b7671a8a590deb7cc8374abde0e","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"89a11b0f472daee2ef11957b2d2af11407b81b7671a8a590deb7cc8374abde0e","first_computed_at":"2026-05-22T01:03:13.811773Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-22T01:03:13.811773Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"8hAph+ghfwedfvbuD9Ej0rqQ5QzZGj4uxDESOz+/1zfmQtKptswUJJA7zEJOyxCFuJMcmC95jkpO1r4+PoumAw==","signature_status":"signed_v1","signed_at":"2026-05-22T01:03:13.812717Z","signed_message":"canonical_sha256_bytes"},"source_id":"2405.17032","source_kind":"arxiv","source_version":4}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:0d4f3c94d344bcdf7ca18500c13bd211cf6830fbc3e32f369cbd69f86f928676","sha256:2df0a5c40d0f08fea72c42fac6afb0a054bd0b86ccb62fa0b8a797aac837b875"],"state_sha256":"b1bc083be3d1ae72625dddfccd7bd35384aa999ef2284b67db9db3e11c7a721c"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"xxe25zBsminKp6e3Lvbgt25pLZzJ58D4FGZ3YIfq7yMXrj9qbaJ2qgruXXpOeMOZPEMIl2AMEGkSukmcR4TSCw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-03T21:45:55.582542Z","bundle_sha256":"5fc2c2972c9fb491078004af938e47fc974c1a0d9e154fd9e81024e42381b11c"}}