{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2010:LWFNR6DMLHQH57MWOTXT4HLDPI","short_pith_number":"pith:LWFNR6DM","canonical_record":{"source":{"id":"1011.5096","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2010-11-23T13:40:56Z","cross_cats_sorted":["stat.ML"],"title_canon_sha256":"91b9cb3edcd3e61b4af0c15296a7d866f24a90d9d78d76cc21022c8bef6b9ca7","abstract_canon_sha256":"80f4a15d247b88454ea527bf95ec17bcb663ae7a6c5eb3492478a9cd2273cfdb"},"schema_version":"1.0"},"canonical_sha256":"5d8ad8f86c59e07efd9674ef3e1d637a09a2ebc437f235ae23957bab95073ec7","source":{"kind":"arxiv","id":"1011.5096","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1011.5096","created_at":"2026-05-18T04:31:52Z"},{"alias_kind":"arxiv_version","alias_value":"1011.5096v1","created_at":"2026-05-18T04:31:52Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1011.5096","created_at":"2026-05-18T04:31:52Z"},{"alias_kind":"pith_short_12","alias_value":"LWFNR6DMLHQH","created_at":"2026-05-18T12:26:10Z"},{"alias_kind":"pith_short_16","alias_value":"LWFNR6DMLHQH57MW","created_at":"2026-05-18T12:26:10Z"},{"alias_kind":"pith_short_8","alias_value":"LWFNR6DM","created_at":"2026-05-18T12:26:10Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2010:LWFNR6DMLHQH57MWOTXT4HLDPI","target":"record","payload":{"canonical_record":{"source":{"id":"1011.5096","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2010-11-23T13:40:56Z","cross_cats_sorted":["stat.ML"],"title_canon_sha256":"91b9cb3edcd3e61b4af0c15296a7d866f24a90d9d78d76cc21022c8bef6b9ca7","abstract_canon_sha256":"80f4a15d247b88454ea527bf95ec17bcb663ae7a6c5eb3492478a9cd2273cfdb"},"schema_version":"1.0"},"canonical_sha256":"5d8ad8f86c59e07efd9674ef3e1d637a09a2ebc437f235ae23957bab95073ec7","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T04:31:52.152416Z","signature_b64":"cEJxnr8JJ7P+nUxae3NvZyOdgfwi3lZKXOqiv68zzV5afarmokYNRKlABjmJh5Y+eoUBrrlkbQMHImVRN/t3Dw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"5d8ad8f86c59e07efd9674ef3e1d637a09a2ebc437f235ae23957bab95073ec7","last_reissued_at":"2026-05-18T04:31:52.151973Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T04:31:52.151973Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1011.5096","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":"2026-05-18T04:31:52Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"UAYiAH/b9s+NfzqXmiauWKIxBdKu+MflRwgbW+NVq9EzKmOTaoIRVrrst8k4xcanXTN0Fmq9S0SM0qHT+qXVBA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-31T21:06:03.875906Z"},"content_sha256":"fccca5734a6695e5bb084fea9b036f5c6136f62aae72fb6379dc4484d991debb","schema_version":"1.0","event_id":"sha256:fccca5734a6695e5bb084fea9b036f5c6136f62aae72fb6379dc4484d991debb"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2010:LWFNR6DMLHQH57MWOTXT4HLDPI","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Evolutionary distances in the twilight zone -- a rational kernel approach","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["stat.ML"],"primary_cat":"q-bio.PE","authors_text":"Benjamin Merget, Florian Markowetz, Frank F\\\"orster, J\\\"org Schultz, Matthias Wolf, Roland F. Schwarz, William Fletcher","submitted_at":"2010-11-23T13:40:56Z","abstract_excerpt":"Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1011.5096","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":"2026-05-18T04:31:52Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Llsyu9PrZfrF20XJ4hOijV60SzWrxXrL/smH8ee/qDyzJJqr89qnkw3FxB2KG0CFUacBjzvk4jXV7wal7k2iAg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-31T21:06:03.876647Z"},"content_sha256":"0409826f6ef7799e3f4051603c8313da463cdb8e6fe851d93ce840a75aaa1afd","schema_version":"1.0","event_id":"sha256:0409826f6ef7799e3f4051603c8313da463cdb8e6fe851d93ce840a75aaa1afd"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/LWFNR6DMLHQH57MWOTXT4HLDPI/bundle.json","state_url":"https://pith.science/pith/LWFNR6DMLHQH57MWOTXT4HLDPI/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/LWFNR6DMLHQH57MWOTXT4HLDPI/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":"2026-05-31T21:06:03Z","links":{"resolver":"https://pith.science/pith/LWFNR6DMLHQH57MWOTXT4HLDPI","bundle":"https://pith.science/pith/LWFNR6DMLHQH57MWOTXT4HLDPI/bundle.json","state":"https://pith.science/pith/LWFNR6DMLHQH57MWOTXT4HLDPI/state.json","well_known_bundle":"https://pith.science/.well-known/pith/LWFNR6DMLHQH57MWOTXT4HLDPI/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2010:LWFNR6DMLHQH57MWOTXT4HLDPI","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":"80f4a15d247b88454ea527bf95ec17bcb663ae7a6c5eb3492478a9cd2273cfdb","cross_cats_sorted":["stat.ML"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2010-11-23T13:40:56Z","title_canon_sha256":"91b9cb3edcd3e61b4af0c15296a7d866f24a90d9d78d76cc21022c8bef6b9ca7"},"schema_version":"1.0","source":{"id":"1011.5096","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1011.5096","created_at":"2026-05-18T04:31:52Z"},{"alias_kind":"arxiv_version","alias_value":"1011.5096v1","created_at":"2026-05-18T04:31:52Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1011.5096","created_at":"2026-05-18T04:31:52Z"},{"alias_kind":"pith_short_12","alias_value":"LWFNR6DMLHQH","created_at":"2026-05-18T12:26:10Z"},{"alias_kind":"pith_short_16","alias_value":"LWFNR6DMLHQH57MW","created_at":"2026-05-18T12:26:10Z"},{"alias_kind":"pith_short_8","alias_value":"LWFNR6DM","created_at":"2026-05-18T12:26:10Z"}],"graph_snapshots":[{"event_id":"sha256:0409826f6ef7799e3f4051603c8313da463cdb8e6fe851d93ce840a75aaa1afd","target":"graph","created_at":"2026-05-18T04:31:52Z","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":"Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons and avoid potential alignment problems. However, in general they are not biologically motivated and ignore our knowledge about the evolution of sequences. Thus, it is still a major open question how to define an evolutionary distance metric between divergent sequences that makes ","authors_text":"Benjamin Merget, Florian Markowetz, Frank F\\\"orster, J\\\"org Schultz, Matthias Wolf, Roland F. Schwarz, William Fletcher","cross_cats":["stat.ML"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2010-11-23T13:40:56Z","title":"Evolutionary distances in the twilight zone -- a rational kernel approach"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1011.5096","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:fccca5734a6695e5bb084fea9b036f5c6136f62aae72fb6379dc4484d991debb","target":"record","created_at":"2026-05-18T04:31:52Z","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":"80f4a15d247b88454ea527bf95ec17bcb663ae7a6c5eb3492478a9cd2273cfdb","cross_cats_sorted":["stat.ML"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2010-11-23T13:40:56Z","title_canon_sha256":"91b9cb3edcd3e61b4af0c15296a7d866f24a90d9d78d76cc21022c8bef6b9ca7"},"schema_version":"1.0","source":{"id":"1011.5096","kind":"arxiv","version":1}},"canonical_sha256":"5d8ad8f86c59e07efd9674ef3e1d637a09a2ebc437f235ae23957bab95073ec7","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"5d8ad8f86c59e07efd9674ef3e1d637a09a2ebc437f235ae23957bab95073ec7","first_computed_at":"2026-05-18T04:31:52.151973Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T04:31:52.151973Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"cEJxnr8JJ7P+nUxae3NvZyOdgfwi3lZKXOqiv68zzV5afarmokYNRKlABjmJh5Y+eoUBrrlkbQMHImVRN/t3Dw==","signature_status":"signed_v1","signed_at":"2026-05-18T04:31:52.152416Z","signed_message":"canonical_sha256_bytes"},"source_id":"1011.5096","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:fccca5734a6695e5bb084fea9b036f5c6136f62aae72fb6379dc4484d991debb","sha256:0409826f6ef7799e3f4051603c8313da463cdb8e6fe851d93ce840a75aaa1afd"],"state_sha256":"b662229d698f90a20bc7a8fab4f6623f8f2c4418cf6a4a9afb6b1ab018c221d2"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"21dHC+q3+rY+JkMu9q/15PSMV1WdxB4Xt967H1W28QRG/jRYm+W6CLGY+W6v7AjoKVuwAaCSila8eWyIm5RdDQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-31T21:06:03.880686Z","bundle_sha256":"e4339789df93c776b028a3d262f5cf2f9a764f3307b0e53bba24869e08f161cc"}}