{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:F4PA45T75BE5XGXX7WXRV33UTC","short_pith_number":"pith:F4PA45T7","canonical_record":{"source":{"id":"2502.10365","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-14T18:43:22Z","cross_cats_sorted":[],"title_canon_sha256":"91af1f9bc8340dbda250c1f416a2369a38d11a82f078f276f5e5b991d1a4179f","abstract_canon_sha256":"f58486ac52870e50c8c6ae04a6fa84ea65de68d012e6cdb4b34db1854edb2ae5"},"schema_version":"1.0"},"canonical_sha256":"2f1e0e767fe849db9af7fdaf1aef7498b5d8e77a183b7464ca836668fcd06f8e","source":{"kind":"arxiv","id":"2502.10365","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.10365","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"arxiv_version","alias_value":"2502.10365v2","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.10365","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"pith_short_12","alias_value":"F4PA45T75BE5","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"pith_short_16","alias_value":"F4PA45T75BE5XGXX","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"pith_short_8","alias_value":"F4PA45T7","created_at":"2026-07-05T10:15:26Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:F4PA45T75BE5XGXX7WXRV33UTC","target":"record","payload":{"canonical_record":{"source":{"id":"2502.10365","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-14T18:43:22Z","cross_cats_sorted":[],"title_canon_sha256":"91af1f9bc8340dbda250c1f416a2369a38d11a82f078f276f5e5b991d1a4179f","abstract_canon_sha256":"f58486ac52870e50c8c6ae04a6fa84ea65de68d012e6cdb4b34db1854edb2ae5"},"schema_version":"1.0"},"canonical_sha256":"2f1e0e767fe849db9af7fdaf1aef7498b5d8e77a183b7464ca836668fcd06f8e","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:15:26.950231Z","signature_b64":"bgDkgHdOwF2UqDjfjy55ocb9T3UxiLD0/S+RdqWIRbWtD0PFhtRwsb/Pa2XYKGsLVgmHMdfXcgFOfd5A3tyeDg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"2f1e0e767fe849db9af7fdaf1aef7498b5d8e77a183b7464ca836668fcd06f8e","last_reissued_at":"2026-07-05T10:15:26.949746Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:15:26.949746Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2502.10365","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":"2026-07-05T10:15:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"//WOl7uswghj4wY2WGWp0MPLeA1NGrhIhYSanuUFQfoWjTVjYHIpg3a1PAPriO0YIB8kDdIo5OQPyrtZqI0IAw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T20:44:49.350724Z"},"content_sha256":"0d3773df39574d578904e4563867c3ef5ad93f4912457029821fe9805e2e3ca8","schema_version":"1.0","event_id":"sha256:0d3773df39574d578904e4563867c3ef5ad93f4912457029821fe9805e2e3ca8"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:F4PA45T75BE5XGXX7WXRV33UTC","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"AffinityFlow: Guided Flows for Antibody Affinity Maturation","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.LG","authors_text":"Can Chen, Chenchao Zhao, Karla-Luise Herpoldt, Marcus Collins, Ron Benson, Shang Shang, Zichen Wang","submitted_at":"2025-02-14T18:43:22Z","abstract_excerpt":"Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity.This paper explores a sequence-only scenario for affinity maturation, using solely antibody and antigen sequences. Recently AlphaFlow wraps AlphaFold within flow matching to generate diverse protein structures, enabling a sequence-conditioned generative model of structure. Building on this, we propose an alternating optimization framework that (1) fixes the sequence to guide structure generation toward high binding affinity using a str"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.10365","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":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2502.10365/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":"2026-07-05T10:15:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"b539FA/AS9jgITOelFTNpdB03eEbiaecPC2kcbekaBn0FlUwUcFEZVdEmanQJ6wx8IvceGpxc4ocbZ5YQh9CBg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T20:44:49.351234Z"},"content_sha256":"6d71274e30c31c6dbdc82a8b56f0234c0023ba847f3d699fae1318bbead56ed4","schema_version":"1.0","event_id":"sha256:6d71274e30c31c6dbdc82a8b56f0234c0023ba847f3d699fae1318bbead56ed4"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/F4PA45T75BE5XGXX7WXRV33UTC/bundle.json","state_url":"https://pith.science/pith/F4PA45T75BE5XGXX7WXRV33UTC/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/F4PA45T75BE5XGXX7WXRV33UTC/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":"2026-08-08T20:44:49Z","links":{"resolver":"https://pith.science/pith/F4PA45T75BE5XGXX7WXRV33UTC","bundle":"https://pith.science/pith/F4PA45T75BE5XGXX7WXRV33UTC/bundle.json","state":"https://pith.science/pith/F4PA45T75BE5XGXX7WXRV33UTC/state.json","well_known_bundle":"https://pith.science/.well-known/pith/F4PA45T75BE5XGXX7WXRV33UTC/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:F4PA45T75BE5XGXX7WXRV33UTC","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":"f58486ac52870e50c8c6ae04a6fa84ea65de68d012e6cdb4b34db1854edb2ae5","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-14T18:43:22Z","title_canon_sha256":"91af1f9bc8340dbda250c1f416a2369a38d11a82f078f276f5e5b991d1a4179f"},"schema_version":"1.0","source":{"id":"2502.10365","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2502.10365","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"arxiv_version","alias_value":"2502.10365v2","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2502.10365","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"pith_short_12","alias_value":"F4PA45T75BE5","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"pith_short_16","alias_value":"F4PA45T75BE5XGXX","created_at":"2026-07-05T10:15:26Z"},{"alias_kind":"pith_short_8","alias_value":"F4PA45T7","created_at":"2026-07-05T10:15:26Z"}],"graph_snapshots":[{"event_id":"sha256:6d71274e30c31c6dbdc82a8b56f0234c0023ba847f3d699fae1318bbead56ed4","target":"graph","created_at":"2026-07-05T10:15:26Z","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"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2502.10365/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Antibodies are widely used as therapeutics, but their development requires costly affinity maturation, involving iterative mutations to enhance binding affinity.This paper explores a sequence-only scenario for affinity maturation, using solely antibody and antigen sequences. Recently AlphaFlow wraps AlphaFold within flow matching to generate diverse protein structures, enabling a sequence-conditioned generative model of structure. Building on this, we propose an alternating optimization framework that (1) fixes the sequence to guide structure generation toward high binding affinity using a str","authors_text":"Can Chen, Chenchao Zhao, Karla-Luise Herpoldt, Marcus Collins, Ron Benson, Shang Shang, Zichen Wang","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-14T18:43:22Z","title":"AffinityFlow: Guided Flows for Antibody Affinity Maturation"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2502.10365","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":"sha256:0d3773df39574d578904e4563867c3ef5ad93f4912457029821fe9805e2e3ca8","target":"record","created_at":"2026-07-05T10:15:26Z","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":"f58486ac52870e50c8c6ae04a6fa84ea65de68d012e6cdb4b34db1854edb2ae5","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2025-02-14T18:43:22Z","title_canon_sha256":"91af1f9bc8340dbda250c1f416a2369a38d11a82f078f276f5e5b991d1a4179f"},"schema_version":"1.0","source":{"id":"2502.10365","kind":"arxiv","version":2}},"canonical_sha256":"2f1e0e767fe849db9af7fdaf1aef7498b5d8e77a183b7464ca836668fcd06f8e","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"2f1e0e767fe849db9af7fdaf1aef7498b5d8e77a183b7464ca836668fcd06f8e","first_computed_at":"2026-07-05T10:15:26.949746Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:15:26.949746Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"bgDkgHdOwF2UqDjfjy55ocb9T3UxiLD0/S+RdqWIRbWtD0PFhtRwsb/Pa2XYKGsLVgmHMdfXcgFOfd5A3tyeDg==","signature_status":"signed_v1","signed_at":"2026-07-05T10:15:26.950231Z","signed_message":"canonical_sha256_bytes"},"source_id":"2502.10365","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:0d3773df39574d578904e4563867c3ef5ad93f4912457029821fe9805e2e3ca8","sha256:6d71274e30c31c6dbdc82a8b56f0234c0023ba847f3d699fae1318bbead56ed4"],"state_sha256":"2cfd29dd478417b35987fba9e52b97e32d1c9096fd04413fa8b8cbc2ec8f2171"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"/Th3CNfwRIsp4k8a9ypNvcgrK7oG0hM5OS6iV8Or2DKS4JZGiPyLJdVrxeeRO4xfbA9MbzriHP3H+mnJiO94AQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-08T20:44:49.355801Z","bundle_sha256":"0c3117ee15dcefa1557a2a465d43121930d9e47a3a46f009baa207faa3262e0a"}}