{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:AMAOEW2RBUHPQVYU3BSH3URTKJ","short_pith_number":"pith:AMAOEW2R","canonical_record":{"source":{"id":"2502.19395","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-11T13:29:49Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"d9e84656ea6c176e411ed38a2079e50b32f63827480382f587b34b32176070a5","abstract_canon_sha256":"e715c44ce22e7480ac902ad98708ac915e3a263cc55996d415e38acd1ba3b6c6"},"schema_version":"1.0"},"canonical_sha256":"0300e25b510d0ef85714d8647dd233524da28106821b13cb0b7b316e518a749e","source":{"kind":"arxiv","id":"2502.19395","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.19395","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"arxiv_version","alias_value":"2502.19395v1","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.19395","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_12","alias_value":"AMAOEW2RBUHP","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_16","alias_value":"AMAOEW2RBUHPQVYU","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_8","alias_value":"AMAOEW2R","created_at":"2026-07-05T10:20:31Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:AMAOEW2RBUHPQVYU3BSH3URTKJ","target":"record","payload":{"canonical_record":{"source":{"id":"2502.19395","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-11T13:29:49Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"d9e84656ea6c176e411ed38a2079e50b32f63827480382f587b34b32176070a5","abstract_canon_sha256":"e715c44ce22e7480ac902ad98708ac915e3a263cc55996d415e38acd1ba3b6c6"},"schema_version":"1.0"},"canonical_sha256":"0300e25b510d0ef85714d8647dd233524da28106821b13cb0b7b316e518a749e","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:20:31.505914Z","signature_b64":"mhCoB0vLjcWqhTnGfRJsvs83UmhqPjXz7l2324QTrluqEC9Yjkt/zoCr+hKoEq+dgUKa57az59+LKgUSSS3cCA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"0300e25b510d0ef85714d8647dd233524da28106821b13cb0b7b316e518a749e","last_reissued_at":"2026-07-05T10:20:31.505403Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:20:31.505403Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2502.19395","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":"2026-07-05T10:20:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5z1Kbx6ceQHceYSWfQmdVRBVd76pu12oPNtA1m6PuYEsodqISXvmoWC/UWJST97MOBjheGZcjXqn7F2FXy5HDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T22:57:43.453223Z"},"content_sha256":"3cb68e53dfc95ad761dc2e9542ecafc9c07abf5ff1fa7a9855a0f02d4ec0d0b1","schema_version":"1.0","event_id":"sha256:3cb68e53dfc95ad761dc2e9542ecafc9c07abf5ff1fa7a9855a0f02d4ec0d0b1"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:AMAOEW2RBUHPQVYU3BSH3URTKJ","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Fast and Accurate Antibody Sequence Design via Structure Retrieval","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.LG"],"primary_cat":"q-bio.BM","authors_text":"Biaobin Jiang, Kangfei Zhao, Kun Xie, Ningqiao Huang, Peilin Zhao, Sibo Wang, Wei Liu, Xingyi Zhang","submitted_at":"2025-02-11T13:29:49Z","abstract_excerpt":"Recent advancements in protein design have leveraged diffusion models to generate structural scaffolds, followed by a process known as protein inverse folding, which involves sequence inference on these scaffolds. However, these methodologies face significant challenges when applied to hyper-variable structures such as antibody Complementarity-Determining Regions (CDRs), where sequence inference frequently results in non-functional sequences due to hallucinations. Distinguished from prevailing protein inverse folding approaches, this paper introduces Igseek, a novel structure-retrieval framewo"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.19395","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/2502.19395/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":"2026-07-05T10:20:31Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"a/t/eYP0zvTV+Mkd6d877MD351sbI+8arrFPbyT8LTBnvpGK13+I9bFiOPwBhmI9tn2tqTGdTftZOj0X8CZcCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T22:57:43.453715Z"},"content_sha256":"a2bb654cb52f5a7a2aceb040c8bd719ac1a1d2082a573b9206b144f69e6b20d7","schema_version":"1.0","event_id":"sha256:a2bb654cb52f5a7a2aceb040c8bd719ac1a1d2082a573b9206b144f69e6b20d7"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/AMAOEW2RBUHPQVYU3BSH3URTKJ/bundle.json","state_url":"https://pith.science/pith/AMAOEW2RBUHPQVYU3BSH3URTKJ/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/AMAOEW2RBUHPQVYU3BSH3URTKJ/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":"2026-08-08T22:57:43Z","links":{"resolver":"https://pith.science/pith/AMAOEW2RBUHPQVYU3BSH3URTKJ","bundle":"https://pith.science/pith/AMAOEW2RBUHPQVYU3BSH3URTKJ/bundle.json","state":"https://pith.science/pith/AMAOEW2RBUHPQVYU3BSH3URTKJ/state.json","well_known_bundle":"https://pith.science/.well-known/pith/AMAOEW2RBUHPQVYU3BSH3URTKJ/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:AMAOEW2RBUHPQVYU3BSH3URTKJ","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":"e715c44ce22e7480ac902ad98708ac915e3a263cc55996d415e38acd1ba3b6c6","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-11T13:29:49Z","title_canon_sha256":"d9e84656ea6c176e411ed38a2079e50b32f63827480382f587b34b32176070a5"},"schema_version":"1.0","source":{"id":"2502.19395","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.19395","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"arxiv_version","alias_value":"2502.19395v1","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.19395","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_12","alias_value":"AMAOEW2RBUHP","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_16","alias_value":"AMAOEW2RBUHPQVYU","created_at":"2026-07-05T10:20:31Z"},{"alias_kind":"pith_short_8","alias_value":"AMAOEW2R","created_at":"2026-07-05T10:20:31Z"}],"graph_snapshots":[{"event_id":"sha256:a2bb654cb52f5a7a2aceb040c8bd719ac1a1d2082a573b9206b144f69e6b20d7","target":"graph","created_at":"2026-07-05T10:20:31Z","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/2502.19395/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Recent advancements in protein design have leveraged diffusion models to generate structural scaffolds, followed by a process known as protein inverse folding, which involves sequence inference on these scaffolds. However, these methodologies face significant challenges when applied to hyper-variable structures such as antibody Complementarity-Determining Regions (CDRs), where sequence inference frequently results in non-functional sequences due to hallucinations. Distinguished from prevailing protein inverse folding approaches, this paper introduces Igseek, a novel structure-retrieval framewo","authors_text":"Biaobin Jiang, Kangfei Zhao, Kun Xie, Ningqiao Huang, Peilin Zhao, Sibo Wang, Wei Liu, Xingyi Zhang","cross_cats":["cs.LG"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-11T13:29:49Z","title":"Fast and Accurate Antibody Sequence Design via Structure Retrieval"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.19395","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":"sha256:3cb68e53dfc95ad761dc2e9542ecafc9c07abf5ff1fa7a9855a0f02d4ec0d0b1","target":"record","created_at":"2026-07-05T10:20:31Z","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":"e715c44ce22e7480ac902ad98708ac915e3a263cc55996d415e38acd1ba3b6c6","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-11T13:29:49Z","title_canon_sha256":"d9e84656ea6c176e411ed38a2079e50b32f63827480382f587b34b32176070a5"},"schema_version":"1.0","source":{"id":"2502.19395","kind":"arxiv","version":1}},"canonical_sha256":"0300e25b510d0ef85714d8647dd233524da28106821b13cb0b7b316e518a749e","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"0300e25b510d0ef85714d8647dd233524da28106821b13cb0b7b316e518a749e","first_computed_at":"2026-07-05T10:20:31.505403Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:20:31.505403Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"mhCoB0vLjcWqhTnGfRJsvs83UmhqPjXz7l2324QTrluqEC9Yjkt/zoCr+hKoEq+dgUKa57az59+LKgUSSS3cCA==","signature_status":"signed_v1","signed_at":"2026-07-05T10:20:31.505914Z","signed_message":"canonical_sha256_bytes"},"source_id":"2502.19395","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:3cb68e53dfc95ad761dc2e9542ecafc9c07abf5ff1fa7a9855a0f02d4ec0d0b1","sha256:a2bb654cb52f5a7a2aceb040c8bd719ac1a1d2082a573b9206b144f69e6b20d7"],"state_sha256":"cb4f3681bbed9c4e76b7e3599c8a596647613ce0ccd7999d5e38a63d508fc47c"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"BARxOA/BtDTGaonLnKLa/roxn7VYJk4QNclD566/DZCcfB9m1EsQ1Sz+L+FQdBV/MudB8bkWRU7u79DWKS8cBQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-08T22:57:43.457646Z","bundle_sha256":"cf10531ee81c4b62f89d426a07e389d23dad4ce3a6b4069291681694b663608c"}}