{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2011:SFEEJ6KGBQY4LY3EW6DXXLBXKK","short_pith_number":"pith:SFEEJ6KG","canonical_record":{"source":{"id":"1110.6739","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2011-10-31T10:17:52Z","cross_cats_sorted":["cs.CE"],"title_canon_sha256":"3fe49bb28ae0f5e3625a0f50d49d0d99882d09b17ed712139fbe35be6b10ca58","abstract_canon_sha256":"66a62c6939d3822b9001a9b78383c5dd7a922c6bce86c9385cc501409a37b791"},"schema_version":"1.0"},"canonical_sha256":"914844f9460c31c5e364b7877bac375287b4793087b74abd01db2ce1f3448c9d","source":{"kind":"arxiv","id":"1110.6739","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1110.6739","created_at":"2026-05-18T03:52:26Z"},{"alias_kind":"arxiv_version","alias_value":"1110.6739v2","created_at":"2026-05-18T03:52:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1110.6739","created_at":"2026-05-18T03:52:26Z"},{"alias_kind":"pith_short_12","alias_value":"SFEEJ6KGBQY4","created_at":"2026-05-18T12:26:41Z"},{"alias_kind":"pith_short_16","alias_value":"SFEEJ6KGBQY4LY3E","created_at":"2026-05-18T12:26:41Z"},{"alias_kind":"pith_short_8","alias_value":"SFEEJ6KG","created_at":"2026-05-18T12:26:41Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2011:SFEEJ6KGBQY4LY3EW6DXXLBXKK","target":"record","payload":{"canonical_record":{"source":{"id":"1110.6739","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2011-10-31T10:17:52Z","cross_cats_sorted":["cs.CE"],"title_canon_sha256":"3fe49bb28ae0f5e3625a0f50d49d0d99882d09b17ed712139fbe35be6b10ca58","abstract_canon_sha256":"66a62c6939d3822b9001a9b78383c5dd7a922c6bce86c9385cc501409a37b791"},"schema_version":"1.0"},"canonical_sha256":"914844f9460c31c5e364b7877bac375287b4793087b74abd01db2ce1f3448c9d","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:52:26.232731Z","signature_b64":"GzkvNhkMrc+UQAJ6wgWjSSLobaTVSN5GvJdmwvQ+1dDllTdvB0GroiH2xdxgVrrVTmTwjyoXRuY8haJcnkbkAQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"914844f9460c31c5e364b7877bac375287b4793087b74abd01db2ce1f3448c9d","last_reissued_at":"2026-05-18T03:52:26.232187Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:52:26.232187Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1110.6739","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T03:52:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5etFomQ4rfrHll3J7wNiyGK/NgBfMO2R2zKLQSejepSgTh48nNLRcyo7MOzbJAz8ISBUZ7h9W0j9jmWQWRs0Dw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-26T18:55:03.499224Z"},"content_sha256":"a7d074c922f4a043f51b590fc5848cfc1a18061b982f5ee4d1876cba4da0c728","schema_version":"1.0","event_id":"sha256:a7d074c922f4a043f51b590fc5848cfc1a18061b982f5ee4d1876cba4da0c728"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2011:SFEEJ6KGBQY4LY3EW6DXXLBXKK","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"The Binary Perfect Phylogeny with Persistent characters","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.CE"],"primary_cat":"cs.DS","authors_text":"Chiara Braghin, Gabriella Trucco, Paola Bonizzoni, Riccardo Dondi","submitted_at":"2011-10-31T10:17:52Z","abstract_excerpt":"The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem of reconstructing a near perfect phylogeny over a binary set of characters where characters are persistent: characters can be gained and lost at most once. Based on this notion, we define the problem of the Persistent Perfect Phylogeny (referred as P-PP). We restate the P-PP problem as a special case of the Incomplete Directed Perfect Phylogeny, called Inco"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1110.6739","kind":"arxiv","version":2},"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":"2026-05-18T03:52:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"AujL0pB4W/OO+M9lGZVx4uTsTrwIP9gYkZ4aJFrksQbZdXqN5bjyxn/PKNOtAH7pGaq6Ln9AA6Ip7KSIj5icDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-26T18:55:03.499584Z"},"content_sha256":"8ab60a19afc9080cf2e821de63d91c5d42d6c6013d8dd1044f41485c8dfa3229","schema_version":"1.0","event_id":"sha256:8ab60a19afc9080cf2e821de63d91c5d42d6c6013d8dd1044f41485c8dfa3229"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/SFEEJ6KGBQY4LY3EW6DXXLBXKK/bundle.json","state_url":"https://pith.science/pith/SFEEJ6KGBQY4LY3EW6DXXLBXKK/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/SFEEJ6KGBQY4LY3EW6DXXLBXKK/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":"2026-06-26T18:55:03Z","links":{"resolver":"https://pith.science/pith/SFEEJ6KGBQY4LY3EW6DXXLBXKK","bundle":"https://pith.science/pith/SFEEJ6KGBQY4LY3EW6DXXLBXKK/bundle.json","state":"https://pith.science/pith/SFEEJ6KGBQY4LY3EW6DXXLBXKK/state.json","well_known_bundle":"https://pith.science/.well-known/pith/SFEEJ6KGBQY4LY3EW6DXXLBXKK/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2011:SFEEJ6KGBQY4LY3EW6DXXLBXKK","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":"66a62c6939d3822b9001a9b78383c5dd7a922c6bce86c9385cc501409a37b791","cross_cats_sorted":["cs.CE"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2011-10-31T10:17:52Z","title_canon_sha256":"3fe49bb28ae0f5e3625a0f50d49d0d99882d09b17ed712139fbe35be6b10ca58"},"schema_version":"1.0","source":{"id":"1110.6739","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1110.6739","created_at":"2026-05-18T03:52:26Z"},{"alias_kind":"arxiv_version","alias_value":"1110.6739v2","created_at":"2026-05-18T03:52:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1110.6739","created_at":"2026-05-18T03:52:26Z"},{"alias_kind":"pith_short_12","alias_value":"SFEEJ6KGBQY4","created_at":"2026-05-18T12:26:41Z"},{"alias_kind":"pith_short_16","alias_value":"SFEEJ6KGBQY4LY3E","created_at":"2026-05-18T12:26:41Z"},{"alias_kind":"pith_short_8","alias_value":"SFEEJ6KG","created_at":"2026-05-18T12:26:41Z"}],"graph_snapshots":[{"event_id":"sha256:8ab60a19afc9080cf2e821de63d91c5d42d6c6013d8dd1044f41485c8dfa3229","target":"graph","created_at":"2026-05-18T03:52:26Z","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 binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem of reconstructing a near perfect phylogeny over a binary set of characters where characters are persistent: characters can be gained and lost at most once. Based on this notion, we define the problem of the Persistent Perfect Phylogeny (referred as P-PP). We restate the P-PP problem as a special case of the Incomplete Directed Perfect Phylogeny, called Inco","authors_text":"Chiara Braghin, Gabriella Trucco, Paola Bonizzoni, Riccardo Dondi","cross_cats":["cs.CE"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2011-10-31T10:17:52Z","title":"The Binary Perfect Phylogeny with Persistent characters"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1110.6739","kind":"arxiv","version":2},"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:a7d074c922f4a043f51b590fc5848cfc1a18061b982f5ee4d1876cba4da0c728","target":"record","created_at":"2026-05-18T03:52:26Z","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":"66a62c6939d3822b9001a9b78383c5dd7a922c6bce86c9385cc501409a37b791","cross_cats_sorted":["cs.CE"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.DS","submitted_at":"2011-10-31T10:17:52Z","title_canon_sha256":"3fe49bb28ae0f5e3625a0f50d49d0d99882d09b17ed712139fbe35be6b10ca58"},"schema_version":"1.0","source":{"id":"1110.6739","kind":"arxiv","version":2}},"canonical_sha256":"914844f9460c31c5e364b7877bac375287b4793087b74abd01db2ce1f3448c9d","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"914844f9460c31c5e364b7877bac375287b4793087b74abd01db2ce1f3448c9d","first_computed_at":"2026-05-18T03:52:26.232187Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T03:52:26.232187Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"GzkvNhkMrc+UQAJ6wgWjSSLobaTVSN5GvJdmwvQ+1dDllTdvB0GroiH2xdxgVrrVTmTwjyoXRuY8haJcnkbkAQ==","signature_status":"signed_v1","signed_at":"2026-05-18T03:52:26.232731Z","signed_message":"canonical_sha256_bytes"},"source_id":"1110.6739","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:a7d074c922f4a043f51b590fc5848cfc1a18061b982f5ee4d1876cba4da0c728","sha256:8ab60a19afc9080cf2e821de63d91c5d42d6c6013d8dd1044f41485c8dfa3229"],"state_sha256":"95613c0c5b851e5875a3430beb08faf430618fd67a476c9d556bebdc7fe5b8af"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"YeLwbyB0z7rNyVth4QGvNESMAZyMvi3ExUVhNm/S7zi5+fAzQY0gAEnAkyV5/blreJ5nSXLgedMFh00VMjAiAg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-26T18:55:03.501404Z","bundle_sha256":"5ee32e3f1da5201472a1e50e1e2d18f96bc5864044072bcd33dab18a2bded812"}}