{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:DL5GAA77EIDJ36NEEST6VFWONN","short_pith_number":"pith:DL5GAA77","canonical_record":{"source":{"id":"2606.19377","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2026-06-12T09:46:38Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"4de74319360cde2019131a94e3dca4af455a19c0dbafa89f1dab80e3274f9601","abstract_canon_sha256":"5cedcd3839a832e538a115420957f52a1bd4710e4e3cb6f5449158c68255743f"},"schema_version":"1.0"},"canonical_sha256":"1afa6003ff22069df9a424a7ea96ce6b7db15b0973202588aed6c3e5fefdb052","source":{"kind":"arxiv","id":"2606.19377","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2606.19377","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"arxiv_version","alias_value":"2606.19377v1","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2606.19377","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"pith_short_12","alias_value":"DL5GAA77EIDJ","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"pith_short_16","alias_value":"DL5GAA77EIDJ36NE","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"pith_short_8","alias_value":"DL5GAA77","created_at":"2026-06-19T16:12:23Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:DL5GAA77EIDJ36NEEST6VFWONN","target":"record","payload":{"canonical_record":{"source":{"id":"2606.19377","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2026-06-12T09:46:38Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"4de74319360cde2019131a94e3dca4af455a19c0dbafa89f1dab80e3274f9601","abstract_canon_sha256":"5cedcd3839a832e538a115420957f52a1bd4710e4e3cb6f5449158c68255743f"},"schema_version":"1.0"},"canonical_sha256":"1afa6003ff22069df9a424a7ea96ce6b7db15b0973202588aed6c3e5fefdb052","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-06-19T16:12:23.600390Z","signature_b64":"nWmZYjLsNnLxRySlNRRGMRChxaQYTpUJy1MY2JS3APJO64q9JZycilR1JQ8HVeZ1w1vNZ7nWv0SkAANOkXMFCA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"1afa6003ff22069df9a424a7ea96ce6b7db15b0973202588aed6c3e5fefdb052","last_reissued_at":"2026-06-19T16:12:23.600034Z","signature_status":"signed_v1","first_computed_at":"2026-06-19T16:12:23.600034Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2606.19377","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":"2026-06-19T16:12:23Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"cI+vdeu3r8j+RAEBmhn1VIgUNrYCK2YP+ezTekAF31gs1yi2N8apFc0pPYjEL5rHvKcNgwOn7rg4wXh14QFtAg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-22T15:24:57.647570Z"},"content_sha256":"8ed3a24679bef2ac0faa3c4c77ed6d18428e7f27d34c29c5580ad1cef89a44da","schema_version":"1.0","event_id":"sha256:8ed3a24679bef2ac0faa3c4c77ed6d18428e7f27d34c29c5580ad1cef89a44da"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:DL5GAA77EIDJ36NEEST6VFWONN","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Emyx: Fast and efficient all-atom protein generation","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"cs.LG","authors_text":"Andrew L. Hopkins, Christian D. Madsen, Constantin Schneider, Edward O. Pyzer-Knapp, Matteo P. Ferla, Nicholas B. Woodall, Nicholas J. Williams, Ruby Sedgwick, Ward Haddadin","submitted_at":"2026-06-12T09:46:38Z","abstract_excerpt":"Computational enzyme design requires generating proteins that scaffold catalytic residues and ligands, a task that demands both geometric accuracy and structural diversity from the underlying generative model. Current all-atom generators inherit expensive architectures from structure prediction, leading to high training costs and limited sample diversity. We argue that much of this complexity is unnecessary for generators, which condition on sparse geometric constraints rather than rich co-evolutionary signals. Emyx is a 140M-parameter conditional flow matching model that concentrates capacity"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.19377","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/2606.19377/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":"2026-06-19T16:12:23Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"BHB08rFASnWxEU9NF5ZJ4aONcH8QEJuhzjnGH5kRrTzDZKroew3MtmWTnoKPZ1mMdKak3pwHcH3Uy8qRy17zCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-22T15:24:57.647951Z"},"content_sha256":"d2b3743ccb0ce9aaa4d576bac4de180ae3f31c64857f711518591d6496241aef","schema_version":"1.0","event_id":"sha256:d2b3743ccb0ce9aaa4d576bac4de180ae3f31c64857f711518591d6496241aef"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/DL5GAA77EIDJ36NEEST6VFWONN/bundle.json","state_url":"https://pith.science/pith/DL5GAA77EIDJ36NEEST6VFWONN/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/DL5GAA77EIDJ36NEEST6VFWONN/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":"2026-06-22T15:24:57Z","links":{"resolver":"https://pith.science/pith/DL5GAA77EIDJ36NEEST6VFWONN","bundle":"https://pith.science/pith/DL5GAA77EIDJ36NEEST6VFWONN/bundle.json","state":"https://pith.science/pith/DL5GAA77EIDJ36NEEST6VFWONN/state.json","well_known_bundle":"https://pith.science/.well-known/pith/DL5GAA77EIDJ36NEEST6VFWONN/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:DL5GAA77EIDJ36NEEST6VFWONN","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":"5cedcd3839a832e538a115420957f52a1bd4710e4e3cb6f5449158c68255743f","cross_cats_sorted":["cs.AI"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2026-06-12T09:46:38Z","title_canon_sha256":"4de74319360cde2019131a94e3dca4af455a19c0dbafa89f1dab80e3274f9601"},"schema_version":"1.0","source":{"id":"2606.19377","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2606.19377","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"arxiv_version","alias_value":"2606.19377v1","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2606.19377","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"pith_short_12","alias_value":"DL5GAA77EIDJ","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"pith_short_16","alias_value":"DL5GAA77EIDJ36NE","created_at":"2026-06-19T16:12:23Z"},{"alias_kind":"pith_short_8","alias_value":"DL5GAA77","created_at":"2026-06-19T16:12:23Z"}],"graph_snapshots":[{"event_id":"sha256:d2b3743ccb0ce9aaa4d576bac4de180ae3f31c64857f711518591d6496241aef","target":"graph","created_at":"2026-06-19T16:12:23Z","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/2606.19377/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Computational enzyme design requires generating proteins that scaffold catalytic residues and ligands, a task that demands both geometric accuracy and structural diversity from the underlying generative model. Current all-atom generators inherit expensive architectures from structure prediction, leading to high training costs and limited sample diversity. We argue that much of this complexity is unnecessary for generators, which condition on sparse geometric constraints rather than rich co-evolutionary signals. Emyx is a 140M-parameter conditional flow matching model that concentrates capacity","authors_text":"Andrew L. Hopkins, Christian D. Madsen, Constantin Schneider, Edward O. Pyzer-Knapp, Matteo P. Ferla, Nicholas B. Woodall, Nicholas J. Williams, Ruby Sedgwick, Ward Haddadin","cross_cats":["cs.AI"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2026-06-12T09:46:38Z","title":"Emyx: Fast and efficient all-atom protein generation"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.19377","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":"sha256:8ed3a24679bef2ac0faa3c4c77ed6d18428e7f27d34c29c5580ad1cef89a44da","target":"record","created_at":"2026-06-19T16:12:23Z","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":"5cedcd3839a832e538a115420957f52a1bd4710e4e3cb6f5449158c68255743f","cross_cats_sorted":["cs.AI"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"cs.LG","submitted_at":"2026-06-12T09:46:38Z","title_canon_sha256":"4de74319360cde2019131a94e3dca4af455a19c0dbafa89f1dab80e3274f9601"},"schema_version":"1.0","source":{"id":"2606.19377","kind":"arxiv","version":1}},"canonical_sha256":"1afa6003ff22069df9a424a7ea96ce6b7db15b0973202588aed6c3e5fefdb052","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"1afa6003ff22069df9a424a7ea96ce6b7db15b0973202588aed6c3e5fefdb052","first_computed_at":"2026-06-19T16:12:23.600034Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-06-19T16:12:23.600034Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"nWmZYjLsNnLxRySlNRRGMRChxaQYTpUJy1MY2JS3APJO64q9JZycilR1JQ8HVeZ1w1vNZ7nWv0SkAANOkXMFCA==","signature_status":"signed_v1","signed_at":"2026-06-19T16:12:23.600390Z","signed_message":"canonical_sha256_bytes"},"source_id":"2606.19377","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:8ed3a24679bef2ac0faa3c4c77ed6d18428e7f27d34c29c5580ad1cef89a44da","sha256:d2b3743ccb0ce9aaa4d576bac4de180ae3f31c64857f711518591d6496241aef"],"state_sha256":"2eab071b1f294413b0af50ef69ee38ff586b884c900d61d7e6fb3b2479e75545"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"tKPNcOqYYD8Inz3rz3J1db2n3obHxefE1aovrI+aVpHFIji6xlQJLVQsvKQNLUU+A+Urx95z08zma8JxutL3Ag==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-22T15:24:57.650054Z","bundle_sha256":"014603753a163cba89099659d84f3be58d8c28b30cc8a659b637502df8ce0dc7"}}