{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:54C5UA32ZZQOVQ4WYNHIG36M6N","short_pith_number":"pith:54C5UA32","canonical_record":{"source":{"id":"2607.09998","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-10T21:52:47Z","cross_cats_sorted":["q-bio.BM"],"title_canon_sha256":"0b0231d477e553f602737c3c2429f03c7232fc0e6fb5bd91b3b9d36b7e1e10d9","abstract_canon_sha256":"9c16a955a8893fca57906ae7ba2c5fcfd5671851ef9e2afb68b07a7d430947ad"},"schema_version":"1.0"},"canonical_sha256":"ef05da037ace60eac396c34e836fccf373f540ca860f2c57ca7033d81b5ba804","source":{"kind":"arxiv","id":"2607.09998","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.09998","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"arxiv_version","alias_value":"2607.09998v1","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.09998","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"pith_short_12","alias_value":"54C5UA32ZZQO","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"pith_short_16","alias_value":"54C5UA32ZZQOVQ4W","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"pith_short_8","alias_value":"54C5UA32","created_at":"2026-07-14T00:18:46Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:54C5UA32ZZQOVQ4WYNHIG36M6N","target":"record","payload":{"canonical_record":{"source":{"id":"2607.09998","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-10T21:52:47Z","cross_cats_sorted":["q-bio.BM"],"title_canon_sha256":"0b0231d477e553f602737c3c2429f03c7232fc0e6fb5bd91b3b9d36b7e1e10d9","abstract_canon_sha256":"9c16a955a8893fca57906ae7ba2c5fcfd5671851ef9e2afb68b07a7d430947ad"},"schema_version":"1.0"},"canonical_sha256":"ef05da037ace60eac396c34e836fccf373f540ca860f2c57ca7033d81b5ba804","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-14T00:18:46.905181Z","signature_b64":"u28+ziL0oVLwcXs8C9X5Jgb7Xk1xGuNwn1fjWfmDzPbQuMUAL+11sfFSscrX8TZePBD2+1XSIVhczutZfabXBg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"ef05da037ace60eac396c34e836fccf373f540ca860f2c57ca7033d81b5ba804","last_reissued_at":"2026-07-14T00:18:46.904347Z","signature_status":"signed_v1","first_computed_at":"2026-07-14T00:18:46.904347Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2607.09998","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":"2026-07-14T00:18:46Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"9elg8JZKGgj1QP5IxzzaPp4CFjS6os5gKSfOBEmq1zsDjSpFBixn18vRTa8HKRD7r8Cb1rjL9uN0Z/jubZQbCA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-18T05:27:33.205857Z"},"content_sha256":"7c423049ba26b24fddcfb760d809433c5f0fbf7d969c1f01e962dfad20eedae3","schema_version":"1.0","event_id":"sha256:7c423049ba26b24fddcfb760d809433c5f0fbf7d969c1f01e962dfad20eedae3"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:54C5UA32ZZQOVQ4WYNHIG36M6N","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Vilya-1: An all-atom foundation model for macrocycle structure prediction and design","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","headline":"","cross_cats":["q-bio.BM"],"primary_cat":"cs.LG","authors_text":"Adam P. Moyer, Benjamin D. Sellers, Ivan Anishchanka, Milad Salem, Naozumi Hiranuma, Patrick J. Salveson, Stephen Rettie, Vilya Research: Pascal Sturmfels, Xiaoliang Pan","submitted_at":"2026-07-10T21:52:47Z","abstract_excerpt":"Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space. In this work, we introduce Vilya-1, a deep learning model that addresses two central challenges in macrocycle design: sampling biologically relevant conformations across arbitrary chemistries and predicting key developability properties such as membrane permeability. Vilya-1 operates on a uniform all-atom representation and is trained on heterog"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.09998","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/2607.09998/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":"2026-07-14T00:18:46Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"/XhFeOSHQhpUDHcgCGlXel6a+WLPh+ojubEyip01M7a0WsK2VYA1m2p7H1K80CciUIK/JhqMfbBDpfZzcOdwAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-18T05:27:33.206375Z"},"content_sha256":"7ea6efdb7fae2c7c44c01942acce424c5c326a11146f57d4d7b42134e798facf","schema_version":"1.0","event_id":"sha256:7ea6efdb7fae2c7c44c01942acce424c5c326a11146f57d4d7b42134e798facf"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/54C5UA32ZZQOVQ4WYNHIG36M6N/bundle.json","state_url":"https://pith.science/pith/54C5UA32ZZQOVQ4WYNHIG36M6N/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/54C5UA32ZZQOVQ4WYNHIG36M6N/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":"2026-08-18T05:27:33Z","links":{"resolver":"https://pith.science/pith/54C5UA32ZZQOVQ4WYNHIG36M6N","bundle":"https://pith.science/pith/54C5UA32ZZQOVQ4WYNHIG36M6N/bundle.json","state":"https://pith.science/pith/54C5UA32ZZQOVQ4WYNHIG36M6N/state.json","well_known_bundle":"https://pith.science/.well-known/pith/54C5UA32ZZQOVQ4WYNHIG36M6N/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:54C5UA32ZZQOVQ4WYNHIG36M6N","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":"9c16a955a8893fca57906ae7ba2c5fcfd5671851ef9e2afb68b07a7d430947ad","cross_cats_sorted":["q-bio.BM"],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-10T21:52:47Z","title_canon_sha256":"0b0231d477e553f602737c3c2429f03c7232fc0e6fb5bd91b3b9d36b7e1e10d9"},"schema_version":"1.0","source":{"id":"2607.09998","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.09998","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"arxiv_version","alias_value":"2607.09998v1","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.09998","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"pith_short_12","alias_value":"54C5UA32ZZQO","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"pith_short_16","alias_value":"54C5UA32ZZQOVQ4W","created_at":"2026-07-14T00:18:46Z"},{"alias_kind":"pith_short_8","alias_value":"54C5UA32","created_at":"2026-07-14T00:18:46Z"}],"graph_snapshots":[{"event_id":"sha256:7ea6efdb7fae2c7c44c01942acce424c5c326a11146f57d4d7b42134e798facf","target":"graph","created_at":"2026-07-14T00:18:46Z","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/2607.09998/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space. In this work, we introduce Vilya-1, a deep learning model that addresses two central challenges in macrocycle design: sampling biologically relevant conformations across arbitrary chemistries and predicting key developability properties such as membrane permeability. Vilya-1 operates on a uniform all-atom representation and is trained on heterog","authors_text":"Adam P. Moyer, Benjamin D. Sellers, Ivan Anishchanka, Milad Salem, Naozumi Hiranuma, Patrick J. Salveson, Stephen Rettie, Vilya Research: Pascal Sturmfels, Xiaoliang Pan","cross_cats":["q-bio.BM"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-10T21:52:47Z","title":"Vilya-1: An all-atom foundation model for macrocycle structure prediction and design"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.09998","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":"sha256:7c423049ba26b24fddcfb760d809433c5f0fbf7d969c1f01e962dfad20eedae3","target":"record","created_at":"2026-07-14T00:18:46Z","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":"9c16a955a8893fca57906ae7ba2c5fcfd5671851ef9e2afb68b07a7d430947ad","cross_cats_sorted":["q-bio.BM"],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-10T21:52:47Z","title_canon_sha256":"0b0231d477e553f602737c3c2429f03c7232fc0e6fb5bd91b3b9d36b7e1e10d9"},"schema_version":"1.0","source":{"id":"2607.09998","kind":"arxiv","version":1}},"canonical_sha256":"ef05da037ace60eac396c34e836fccf373f540ca860f2c57ca7033d81b5ba804","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"ef05da037ace60eac396c34e836fccf373f540ca860f2c57ca7033d81b5ba804","first_computed_at":"2026-07-14T00:18:46.904347Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-14T00:18:46.904347Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"u28+ziL0oVLwcXs8C9X5Jgb7Xk1xGuNwn1fjWfmDzPbQuMUAL+11sfFSscrX8TZePBD2+1XSIVhczutZfabXBg==","signature_status":"signed_v1","signed_at":"2026-07-14T00:18:46.905181Z","signed_message":"canonical_sha256_bytes"},"source_id":"2607.09998","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:7c423049ba26b24fddcfb760d809433c5f0fbf7d969c1f01e962dfad20eedae3","sha256:7ea6efdb7fae2c7c44c01942acce424c5c326a11146f57d4d7b42134e798facf"],"state_sha256":"69e1e1fda0324179115d1b089c672dbeba5b592f4d638cd7704e6908505751ed"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"CKaUxA3YMwN+xlCE9hUAXWPk787ferhYUd5mc/RDkOP1WSShJBMsx8XW1T+de+0LbxObmaRgG4aaUBriMvaTBA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-18T05:27:33.211277Z","bundle_sha256":"ba7f5117be33fe0df9f5dded03963c51ce109913f8e50ca05b5160d4f1d4a2d5"}}