{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2014:R5BQKLMIRUY64UXIMIBTZ6TZK6","short_pith_number":"pith:R5BQKLMI","canonical_record":{"source":{"id":"1405.7497","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2014-05-29T08:45:27Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"395e3a1abb2c8247afffefb9cf3820193d4c3417b3d1597f3575d00e7a97400b","abstract_canon_sha256":"187ffa0fdd7c0910160ea8345ad77d68a0dd9dac2539126433ff4b5118c1dd7c"},"schema_version":"1.0"},"canonical_sha256":"8f43052d888d31ee52e862033cfa7957823a9f6f2fc6444f075cb4fb88955957","source":{"kind":"arxiv","id":"1405.7497","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1405.7497","created_at":"2026-05-18T02:50:51Z"},{"alias_kind":"arxiv_version","alias_value":"1405.7497v1","created_at":"2026-05-18T02:50:51Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1405.7497","created_at":"2026-05-18T02:50:51Z"},{"alias_kind":"pith_short_12","alias_value":"R5BQKLMIRUY6","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_16","alias_value":"R5BQKLMIRUY64UXI","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_8","alias_value":"R5BQKLMI","created_at":"2026-05-18T12:28:46Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2014:R5BQKLMIRUY64UXIMIBTZ6TZK6","target":"record","payload":{"canonical_record":{"source":{"id":"1405.7497","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2014-05-29T08:45:27Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"395e3a1abb2c8247afffefb9cf3820193d4c3417b3d1597f3575d00e7a97400b","abstract_canon_sha256":"187ffa0fdd7c0910160ea8345ad77d68a0dd9dac2539126433ff4b5118c1dd7c"},"schema_version":"1.0"},"canonical_sha256":"8f43052d888d31ee52e862033cfa7957823a9f6f2fc6444f075cb4fb88955957","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T02:50:51.122084Z","signature_b64":"ZbwgPGdKAQYaJawSNSGAv/jBYQ4qaQrG/ZEkKXoN37UWgIzGx50Or4GlP5b4U4Irq6jLC4DBpR4ZCkA2rfIGAg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"8f43052d888d31ee52e862033cfa7957823a9f6f2fc6444f075cb4fb88955957","last_reissued_at":"2026-05-18T02:50:51.121622Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T02:50:51.121622Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1405.7497","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":"2026-05-18T02:50:51Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"9qXw0BFyRnqI/3Paeskcza0vIh2eKxmrrYbaXzcBlT8tLfl/Qw3uvyyKoDpINA++5WGRBSBX2G/w0duUPwq1Aw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T05:04:03.713267Z"},"content_sha256":"72739e6c732c21f5bde303edb9f577fc6a71e829a72458fa740448522a626d64","schema_version":"1.0","event_id":"sha256:72739e6c732c21f5bde303edb9f577fc6a71e829a72458fa740448522a626d64"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2014:R5BQKLMIRUY64UXIMIBTZ6TZK6","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Algorithms for the Constrained Perfect Phylogeny with Persistent Characters","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"cs.DS","authors_text":"Anna Paola Carrieri, Gabriella Trucco, Gianluca Della Vedova, Paola Bonizzoni","submitted_at":"2014-05-29T08:45:27Z","abstract_excerpt":"The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect phylogeny model allowing persistent characters, that is characters can be gained and lost at most once. We define a natural generalization of the P-PP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1405.7497","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":""},"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":"2026-05-18T02:50:51Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"W7OPqnGZVk441YetR2Ut0sKM6HeeBn8jVLtpbPnxpryzdcWO1Q4xJ2nMPZvaOyBUpvm7pOxrSS55kJKvP1LtAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-28T05:04:03.713632Z"},"content_sha256":"1ca52bb7ea29d5c931c90019c22c3281e6fd60d2a321db305c3a67a80ccc849c","schema_version":"1.0","event_id":"sha256:1ca52bb7ea29d5c931c90019c22c3281e6fd60d2a321db305c3a67a80ccc849c"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/R5BQKLMIRUY64UXIMIBTZ6TZK6/bundle.json","state_url":"https://pith.science/pith/R5BQKLMIRUY64UXIMIBTZ6TZK6/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/R5BQKLMIRUY64UXIMIBTZ6TZK6/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":"2026-05-28T05:04:03Z","links":{"resolver":"https://pith.science/pith/R5BQKLMIRUY64UXIMIBTZ6TZK6","bundle":"https://pith.science/pith/R5BQKLMIRUY64UXIMIBTZ6TZK6/bundle.json","state":"https://pith.science/pith/R5BQKLMIRUY64UXIMIBTZ6TZK6/state.json","well_known_bundle":"https://pith.science/.well-known/pith/R5BQKLMIRUY64UXIMIBTZ6TZK6/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2014:R5BQKLMIRUY64UXIMIBTZ6TZK6","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":"187ffa0fdd7c0910160ea8345ad77d68a0dd9dac2539126433ff4b5118c1dd7c","cross_cats_sorted":["q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2014-05-29T08:45:27Z","title_canon_sha256":"395e3a1abb2c8247afffefb9cf3820193d4c3417b3d1597f3575d00e7a97400b"},"schema_version":"1.0","source":{"id":"1405.7497","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1405.7497","created_at":"2026-05-18T02:50:51Z"},{"alias_kind":"arxiv_version","alias_value":"1405.7497v1","created_at":"2026-05-18T02:50:51Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1405.7497","created_at":"2026-05-18T02:50:51Z"},{"alias_kind":"pith_short_12","alias_value":"R5BQKLMIRUY6","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_16","alias_value":"R5BQKLMIRUY64UXI","created_at":"2026-05-18T12:28:46Z"},{"alias_kind":"pith_short_8","alias_value":"R5BQKLMI","created_at":"2026-05-18T12:28:46Z"}],"graph_snapshots":[{"event_id":"sha256:1ca52bb7ea29d5c931c90019c22c3281e6fd60d2a321db305c3a67a80ccc849c","target":"graph","created_at":"2026-05-18T02:50:51Z","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"},"paper":{"abstract_excerpt":"The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect phylogeny model allowing persistent characters, that is characters can be gained and lost at most once. We define a natural generalization of the P-PP problem obtained by requiring that for some pairs (character, species), neither the species nor any of its ancestors can have the character. In other words, some characters cannot be persistent for some species. This","authors_text":"Anna Paola Carrieri, Gabriella Trucco, Gianluca Della Vedova, Paola Bonizzoni","cross_cats":["q-bio.QM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2014-05-29T08:45:27Z","title":"Algorithms for the Constrained Perfect Phylogeny with Persistent Characters"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1405.7497","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":"sha256:72739e6c732c21f5bde303edb9f577fc6a71e829a72458fa740448522a626d64","target":"record","created_at":"2026-05-18T02:50:51Z","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":"187ffa0fdd7c0910160ea8345ad77d68a0dd9dac2539126433ff4b5118c1dd7c","cross_cats_sorted":["q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2014-05-29T08:45:27Z","title_canon_sha256":"395e3a1abb2c8247afffefb9cf3820193d4c3417b3d1597f3575d00e7a97400b"},"schema_version":"1.0","source":{"id":"1405.7497","kind":"arxiv","version":1}},"canonical_sha256":"8f43052d888d31ee52e862033cfa7957823a9f6f2fc6444f075cb4fb88955957","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"8f43052d888d31ee52e862033cfa7957823a9f6f2fc6444f075cb4fb88955957","first_computed_at":"2026-05-18T02:50:51.121622Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T02:50:51.121622Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"ZbwgPGdKAQYaJawSNSGAv/jBYQ4qaQrG/ZEkKXoN37UWgIzGx50Or4GlP5b4U4Irq6jLC4DBpR4ZCkA2rfIGAg==","signature_status":"signed_v1","signed_at":"2026-05-18T02:50:51.122084Z","signed_message":"canonical_sha256_bytes"},"source_id":"1405.7497","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:72739e6c732c21f5bde303edb9f577fc6a71e829a72458fa740448522a626d64","sha256:1ca52bb7ea29d5c931c90019c22c3281e6fd60d2a321db305c3a67a80ccc849c"],"state_sha256":"a550ecda075d356a5901652e1ce276cf93039919bf54e4be9d7472dac1904902"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"3QZDhaf5bkGICySIQdjL+Vukw7mZcjc9O5Wk3Ao4keORPt1nyHiE2oSy/LdjAHRl0FthYnlYmANqtzSMw1kzAA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-28T05:04:03.715602Z","bundle_sha256":"a2f6349b455da6e267ddf429b2ac8d397281312ccdc612bc24e899ff8cd29512"}}