{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:2J2LXZDCRMK54ORZTWQSBR4G65","short_pith_number":"pith:2J2LXZDC","canonical_record":{"source":{"id":"2608.01092","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.AI","submitted_at":"2026-08-02T08:48:07Z","cross_cats_sorted":[],"title_canon_sha256":"9fbf7089f1fc90877694d3111e0a96815e3f12409e8a98c45a9b366341992238","abstract_canon_sha256":"30c4bb3ee8c00df0809efe53346103fd0f0a8145aec89b3fc3e652b9162f70f6"},"schema_version":"1.0"},"canonical_sha256":"d274bbe4628b15de3a399da120c786f7738ae8a2616a11bfb7e759572ae32275","source":{"kind":"arxiv","id":"2608.01092","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2608.01092","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"arxiv_version","alias_value":"2608.01092v1","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2608.01092","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"pith_short_12","alias_value":"2J2LXZDCRMK5","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"pith_short_16","alias_value":"2J2LXZDCRMK54ORZ","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"pith_short_8","alias_value":"2J2LXZDC","created_at":"2026-08-04T01:56:32Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:2J2LXZDCRMK54ORZTWQSBR4G65","target":"record","payload":{"canonical_record":{"source":{"id":"2608.01092","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.AI","submitted_at":"2026-08-02T08:48:07Z","cross_cats_sorted":[],"title_canon_sha256":"9fbf7089f1fc90877694d3111e0a96815e3f12409e8a98c45a9b366341992238","abstract_canon_sha256":"30c4bb3ee8c00df0809efe53346103fd0f0a8145aec89b3fc3e652b9162f70f6"},"schema_version":"1.0"},"canonical_sha256":"d274bbe4628b15de3a399da120c786f7738ae8a2616a11bfb7e759572ae32275","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-08-04T01:56:32.552878Z","signature_b64":"CbBDTcKYUBcV2SkHx2yccKRbbVFD2IWu29DeIxa9QnQTvg2oCJifSw7Q71PltBQa7l8PZQ7EILgfXaVVIa+QDA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"d274bbe4628b15de3a399da120c786f7738ae8a2616a11bfb7e759572ae32275","last_reissued_at":"2026-08-04T01:56:32.551467Z","signature_status":"signed_v1","first_computed_at":"2026-08-04T01:56:32.551467Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2608.01092","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":"2026-08-04T01:56:32Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"bErpcEGvuwbCGr3FchIUGRFqGaTxYvymeNhglrTC+HyRmOoblsS6qdxw758tt4RzS1jfruyqnWY6x3eK0ConCw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-17T04:38:30.132794Z"},"content_sha256":"a080c125b369a3a00f36144ac956355b9d3da69576055ae636b3decc38028df2","schema_version":"1.0","event_id":"sha256:a080c125b369a3a00f36144ac956355b9d3da69576055ae636b3decc38028df2"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:2J2LXZDCRMK54ORZTWQSBR4G65","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.AI","authors_text":"Chuanliu Fan, Guohong Fu, Junjie Wu, Nan Yu","submitted_at":"2026-08-02T08:48:07Z","abstract_excerpt":"Antibody-specific epitope prediction aims to identify which antigen residues are recognized by a given antibody, a task that depends on the three-dimensional complementarity between antibody CDRs and the antigen surface. Existing methods usually leverage PLM embeddings and inject structure through additional graph, surface, or point-cloud encoders, where the positional mechanism inside attention remains largely tied to one-dimensional sequence order. For proteins, the analogue of a token offset is not only sequence separation, but also the three-dimensional displacement between residues after "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2608.01092","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/2608.01092/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":"2026-08-04T01:56:32Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"4E8Oun+zUCbmoOjUcWTTrGWAx03SFdIvo++N1OZw5izL7/3Bc37l2ftpwC1eckRpUnCsBp1E/TG1Rm65Xs9GCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-17T04:38:30.133633Z"},"content_sha256":"e0ca8787161ecd3f1b61476c96169d25fdd60247e6ec32662b66da3ebf5cae8b","schema_version":"1.0","event_id":"sha256:e0ca8787161ecd3f1b61476c96169d25fdd60247e6ec32662b66da3ebf5cae8b"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/2J2LXZDCRMK54ORZTWQSBR4G65/bundle.json","state_url":"https://pith.science/pith/2J2LXZDCRMK54ORZTWQSBR4G65/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/2J2LXZDCRMK54ORZTWQSBR4G65/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":"2026-08-17T04:38:30Z","links":{"resolver":"https://pith.science/pith/2J2LXZDCRMK54ORZTWQSBR4G65","bundle":"https://pith.science/pith/2J2LXZDCRMK54ORZTWQSBR4G65/bundle.json","state":"https://pith.science/pith/2J2LXZDCRMK54ORZTWQSBR4G65/state.json","well_known_bundle":"https://pith.science/.well-known/pith/2J2LXZDCRMK54ORZTWQSBR4G65/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:2J2LXZDCRMK54ORZTWQSBR4G65","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":"30c4bb3ee8c00df0809efe53346103fd0f0a8145aec89b3fc3e652b9162f70f6","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.AI","submitted_at":"2026-08-02T08:48:07Z","title_canon_sha256":"9fbf7089f1fc90877694d3111e0a96815e3f12409e8a98c45a9b366341992238"},"schema_version":"1.0","source":{"id":"2608.01092","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2608.01092","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"arxiv_version","alias_value":"2608.01092v1","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2608.01092","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"pith_short_12","alias_value":"2J2LXZDCRMK5","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"pith_short_16","alias_value":"2J2LXZDCRMK54ORZ","created_at":"2026-08-04T01:56:32Z"},{"alias_kind":"pith_short_8","alias_value":"2J2LXZDC","created_at":"2026-08-04T01:56:32Z"}],"graph_snapshots":[{"event_id":"sha256:e0ca8787161ecd3f1b61476c96169d25fdd60247e6ec32662b66da3ebf5cae8b","target":"graph","created_at":"2026-08-04T01:56:32Z","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/2608.01092/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Antibody-specific epitope prediction aims to identify which antigen residues are recognized by a given antibody, a task that depends on the three-dimensional complementarity between antibody CDRs and the antigen surface. Existing methods usually leverage PLM embeddings and inject structure through additional graph, surface, or point-cloud encoders, where the positional mechanism inside attention remains largely tied to one-dimensional sequence order. For proteins, the analogue of a token offset is not only sequence separation, but also the three-dimensional displacement between residues after ","authors_text":"Chuanliu Fan, Guohong Fu, Junjie Wu, Nan Yu","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.AI","submitted_at":"2026-08-02T08:48:07Z","title":"Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2608.01092","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:a080c125b369a3a00f36144ac956355b9d3da69576055ae636b3decc38028df2","target":"record","created_at":"2026-08-04T01:56:32Z","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":"30c4bb3ee8c00df0809efe53346103fd0f0a8145aec89b3fc3e652b9162f70f6","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.AI","submitted_at":"2026-08-02T08:48:07Z","title_canon_sha256":"9fbf7089f1fc90877694d3111e0a96815e3f12409e8a98c45a9b366341992238"},"schema_version":"1.0","source":{"id":"2608.01092","kind":"arxiv","version":1}},"canonical_sha256":"d274bbe4628b15de3a399da120c786f7738ae8a2616a11bfb7e759572ae32275","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"d274bbe4628b15de3a399da120c786f7738ae8a2616a11bfb7e759572ae32275","first_computed_at":"2026-08-04T01:56:32.551467Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-08-04T01:56:32.551467Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"CbBDTcKYUBcV2SkHx2yccKRbbVFD2IWu29DeIxa9QnQTvg2oCJifSw7Q71PltBQa7l8PZQ7EILgfXaVVIa+QDA==","signature_status":"signed_v1","signed_at":"2026-08-04T01:56:32.552878Z","signed_message":"canonical_sha256_bytes"},"source_id":"2608.01092","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:a080c125b369a3a00f36144ac956355b9d3da69576055ae636b3decc38028df2","sha256:e0ca8787161ecd3f1b61476c96169d25fdd60247e6ec32662b66da3ebf5cae8b"],"state_sha256":"369c5974f5865feca0185848b5b597949c4b37b382d5d0050c75e1ff125659cb"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"kXLfY32882UCgtXRv2xA+dNTvzvodG45Dc67VnUzBPF3F2n8SLtjJDRfvDyMGpaitjDdUcs9VHz4gcZ9yG5aBQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-17T04:38:30.195754Z","bundle_sha256":"b38bd9ed006ae2146ed4408c3e9d92e92eccc673d1aa974df28b4d9fae7dcfc3"}}