{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2026:ZRYZCNHSA4E3H2BPWSHFGDJQNF","short_pith_number":"pith:ZRYZCNHS","schema_version":"1.0","canonical_sha256":"cc719134f20709b3e82fb48e530d30694f977687eb9b696b9155fdbc635a4426","source":{"kind":"arxiv","id":"2606.04551","version":1},"attestation_state":"computed","paper":{"title":"Quasi-birth-and-death processes evolving within trees: Applications to comparative phylogenetics","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["math.PR"],"primary_cat":"q-bio.PE","authors_text":"Barbara R. Holland, Habtu Kiros Nigus, Malgorzata M. O'Reilly","submitted_at":"2026-06-03T07:38:16Z","abstract_excerpt":"We consider a quasi-birth-and-process (QBD) that duplicates itself at some fixed times within a tree that contains information about duplication times and potentially partially observed states. We analyse a continuous trait by discretising it to obtain the QBD level variable. Then, the phase variable is used to model the dynamics of the underlying environment.\n  Here, we extend the framework of Soewongsono et al. to enable a more general analysis. We develop an efficient recursive algorithm for computing the likelihood of an observed tree under this model and construct several numerical exampl"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"2606.04551","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2026-06-03T07:38:16Z","cross_cats_sorted":["math.PR"],"title_canon_sha256":"a92caef144d8546236f68d57dc3ee87a072376f2e50ff5989032dad6fe95f840","abstract_canon_sha256":"73fddea3caa1f1f3f4f4b9d2ce53774808e5851d4c643bac314b31e262ea2920"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-06-04T01:09:17.664201Z","signature_b64":"TyfQx76DPhNt1MTsTGb4jsUYf0q/PMkI45fLRDmaoxXPmxt8r4qKMlNcMwkYR44IgbvkRswPYj6Gnl5qJuISDA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"cc719134f20709b3e82fb48e530d30694f977687eb9b696b9155fdbc635a4426","last_reissued_at":"2026-06-04T01:09:17.663396Z","signature_status":"signed_v1","first_computed_at":"2026-06-04T01:09:17.663396Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Quasi-birth-and-death processes evolving within trees: Applications to comparative phylogenetics","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["math.PR"],"primary_cat":"q-bio.PE","authors_text":"Barbara R. Holland, Habtu Kiros Nigus, Malgorzata M. O'Reilly","submitted_at":"2026-06-03T07:38:16Z","abstract_excerpt":"We consider a quasi-birth-and-process (QBD) that duplicates itself at some fixed times within a tree that contains information about duplication times and potentially partially observed states. We analyse a continuous trait by discretising it to obtain the QBD level variable. Then, the phase variable is used to model the dynamics of the underlying environment.\n  Here, we extend the framework of Soewongsono et al. to enable a more general analysis. We develop an efficient recursive algorithm for computing the likelihood of an observed tree under this model and construct several numerical exampl"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.04551","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/2606.04551/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"},"aliases":[{"alias_kind":"arxiv","alias_value":"2606.04551","created_at":"2026-06-04T01:09:17.663527+00:00"},{"alias_kind":"arxiv_version","alias_value":"2606.04551v1","created_at":"2026-06-04T01:09:17.663527+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2606.04551","created_at":"2026-06-04T01:09:17.663527+00:00"},{"alias_kind":"pith_short_12","alias_value":"ZRYZCNHSA4E3","created_at":"2026-06-04T01:09:17.663527+00:00"},{"alias_kind":"pith_short_16","alias_value":"ZRYZCNHSA4E3H2BP","created_at":"2026-06-04T01:09:17.663527+00:00"},{"alias_kind":"pith_short_8","alias_value":"ZRYZCNHS","created_at":"2026-06-04T01:09:17.663527+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF","json":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF.json","graph_json":"https://pith.science/api/pith-number/ZRYZCNHSA4E3H2BPWSHFGDJQNF/graph.json","events_json":"https://pith.science/api/pith-number/ZRYZCNHSA4E3H2BPWSHFGDJQNF/events.json","paper":"https://pith.science/paper/ZRYZCNHS"},"agent_actions":{"view_html":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF","download_json":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF.json","view_paper":"https://pith.science/paper/ZRYZCNHS","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2606.04551&json=true","fetch_graph":"https://pith.science/api/pith-number/ZRYZCNHSA4E3H2BPWSHFGDJQNF/graph.json","fetch_events":"https://pith.science/api/pith-number/ZRYZCNHSA4E3H2BPWSHFGDJQNF/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF/action/timestamp_anchor","attest_storage":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF/action/storage_attestation","attest_author":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF/action/author_attestation","sign_citation":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF/action/citation_signature","submit_replication":"https://pith.science/pith/ZRYZCNHSA4E3H2BPWSHFGDJQNF/action/replication_record"}},"created_at":"2026-06-04T01:09:17.663527+00:00","updated_at":"2026-06-04T01:09:17.663527+00:00"}