{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:7F2JVWFHFPZLAOATPQAOAGAECV","short_pith_number":"pith:7F2JVWFH","canonical_record":{"source":{"id":"2607.25156","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-28T00:01:54Z","cross_cats_sorted":[],"title_canon_sha256":"d4af7a2228947412a26c84c2fec82877b72e17797ec37985ae25af5eb0d53d1c","abstract_canon_sha256":"e0daed6aab0170ca975aab57f1f7ef662a8901b0876c5e0ad26cd40eea248093"},"schema_version":"1.0"},"canonical_sha256":"f9749ad8a72bf2b038137c00e0180415637f572b2e337f48fa311e3a7bf3b74d","source":{"kind":"arxiv","id":"2607.25156","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.25156","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"arxiv_version","alias_value":"2607.25156v1","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.25156","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"pith_short_12","alias_value":"7F2JVWFHFPZL","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"pith_short_16","alias_value":"7F2JVWFHFPZLAOAT","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"pith_short_8","alias_value":"7F2JVWFH","created_at":"2026-07-29T00:25:05Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:7F2JVWFHFPZLAOATPQAOAGAECV","target":"record","payload":{"canonical_record":{"source":{"id":"2607.25156","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-28T00:01:54Z","cross_cats_sorted":[],"title_canon_sha256":"d4af7a2228947412a26c84c2fec82877b72e17797ec37985ae25af5eb0d53d1c","abstract_canon_sha256":"e0daed6aab0170ca975aab57f1f7ef662a8901b0876c5e0ad26cd40eea248093"},"schema_version":"1.0"},"canonical_sha256":"f9749ad8a72bf2b038137c00e0180415637f572b2e337f48fa311e3a7bf3b74d","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-29T00:25:05.801292Z","signature_b64":"4uAj3syDlMQedixztf+QwX8Dfx7t8hAupP7ym57U6+hguVykTiTV2smLSQmj+Q0SmqOLDAklr5S/fGKsciBADQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"f9749ad8a72bf2b038137c00e0180415637f572b2e337f48fa311e3a7bf3b74d","last_reissued_at":"2026-07-29T00:25:05.800443Z","signature_status":"signed_v1","first_computed_at":"2026-07-29T00:25:05.800443Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2607.25156","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":"2026-07-29T00:25:05Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"hduzN3mPpGrocNByvrpFgetMiiyV+cL/IK0fqYW1Hs0xJsiQXx/QA73A6A9iAOoY8bq3vzqDM8r8gkImPGqyDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T22:35:35.207361Z"},"content_sha256":"119617298e451b89f6dbb123b745ddf32aa7503837eefca6e81cc3661f1525a9","schema_version":"1.0","event_id":"sha256:119617298e451b89f6dbb123b745ddf32aa7503837eefca6e81cc3661f1525a9"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:7F2JVWFHFPZLAOATPQAOAGAECV","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Accurate structural modeling of chemically diverse molecular interfaces with Vilya-2","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.LG","authors_text":"Adam P. Moyer, Benjamin D. Sellers, Chase A. P. Wood, CJ San Felipe, Ivan Anishchanka, Jeffrey K. Holden, Milad Salem, Naozumi Hiranuma, Patrick J. Salveson, Stephen Rettie, Vilya Research: Pascal Sturmfels","submitted_at":"2026-07-28T00:01:54Z","abstract_excerpt":"Structure-prediction networks built on co-evolutionary statistics have transformed protein-based drug discovery, yet their accuracy does not extend to peptide therapeutics--an increasingly important modality defined by non-canonical residues, macrocyclization, and complex topologies. We introduce Vilya-2, a diffusion transformer that extends the all-atom representation of Vilya-1 from modeling individual molecules to modeling their interactions with protein targets. This all-atom representation enables transfer learning between different molecular types, and delivers highly accurate structural"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.25156","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/2607.25156/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":"2026-07-29T00:25:05Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"H077SBXk1DKZICFdezML1/sC5zm3coG/UEjc1RM1/1eKVOldjWSjcSYCAwIDp+S+YUbWsJ5AshTlyRgN0rLLBg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T22:35:35.207848Z"},"content_sha256":"ca39b05eb56e2bc7d691e263cfbe0fd4bb72f3ca948505658d0f637e2f99133c","schema_version":"1.0","event_id":"sha256:ca39b05eb56e2bc7d691e263cfbe0fd4bb72f3ca948505658d0f637e2f99133c"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/7F2JVWFHFPZLAOATPQAOAGAECV/bundle.json","state_url":"https://pith.science/pith/7F2JVWFHFPZLAOATPQAOAGAECV/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/7F2JVWFHFPZLAOATPQAOAGAECV/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":"2026-08-04T22:35:35Z","links":{"resolver":"https://pith.science/pith/7F2JVWFHFPZLAOATPQAOAGAECV","bundle":"https://pith.science/pith/7F2JVWFHFPZLAOATPQAOAGAECV/bundle.json","state":"https://pith.science/pith/7F2JVWFHFPZLAOATPQAOAGAECV/state.json","well_known_bundle":"https://pith.science/.well-known/pith/7F2JVWFHFPZLAOATPQAOAGAECV/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:7F2JVWFHFPZLAOATPQAOAGAECV","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":"e0daed6aab0170ca975aab57f1f7ef662a8901b0876c5e0ad26cd40eea248093","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-28T00:01:54Z","title_canon_sha256":"d4af7a2228947412a26c84c2fec82877b72e17797ec37985ae25af5eb0d53d1c"},"schema_version":"1.0","source":{"id":"2607.25156","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.25156","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"arxiv_version","alias_value":"2607.25156v1","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.25156","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"pith_short_12","alias_value":"7F2JVWFHFPZL","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"pith_short_16","alias_value":"7F2JVWFHFPZLAOAT","created_at":"2026-07-29T00:25:05Z"},{"alias_kind":"pith_short_8","alias_value":"7F2JVWFH","created_at":"2026-07-29T00:25:05Z"}],"graph_snapshots":[{"event_id":"sha256:ca39b05eb56e2bc7d691e263cfbe0fd4bb72f3ca948505658d0f637e2f99133c","target":"graph","created_at":"2026-07-29T00:25:05Z","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/2607.25156/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Structure-prediction networks built on co-evolutionary statistics have transformed protein-based drug discovery, yet their accuracy does not extend to peptide therapeutics--an increasingly important modality defined by non-canonical residues, macrocyclization, and complex topologies. We introduce Vilya-2, a diffusion transformer that extends the all-atom representation of Vilya-1 from modeling individual molecules to modeling their interactions with protein targets. This all-atom representation enables transfer learning between different molecular types, and delivers highly accurate structural","authors_text":"Adam P. Moyer, Benjamin D. Sellers, Chase A. P. Wood, CJ San Felipe, Ivan Anishchanka, Jeffrey K. Holden, Milad Salem, Naozumi Hiranuma, Patrick J. Salveson, Stephen Rettie, Vilya Research: Pascal Sturmfels","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-28T00:01:54Z","title":"Accurate structural modeling of chemically diverse molecular interfaces with Vilya-2"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.25156","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":"sha256:119617298e451b89f6dbb123b745ddf32aa7503837eefca6e81cc3661f1525a9","target":"record","created_at":"2026-07-29T00:25:05Z","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":"e0daed6aab0170ca975aab57f1f7ef662a8901b0876c5e0ad26cd40eea248093","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"cs.LG","submitted_at":"2026-07-28T00:01:54Z","title_canon_sha256":"d4af7a2228947412a26c84c2fec82877b72e17797ec37985ae25af5eb0d53d1c"},"schema_version":"1.0","source":{"id":"2607.25156","kind":"arxiv","version":1}},"canonical_sha256":"f9749ad8a72bf2b038137c00e0180415637f572b2e337f48fa311e3a7bf3b74d","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"f9749ad8a72bf2b038137c00e0180415637f572b2e337f48fa311e3a7bf3b74d","first_computed_at":"2026-07-29T00:25:05.800443Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-29T00:25:05.800443Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"4uAj3syDlMQedixztf+QwX8Dfx7t8hAupP7ym57U6+hguVykTiTV2smLSQmj+Q0SmqOLDAklr5S/fGKsciBADQ==","signature_status":"signed_v1","signed_at":"2026-07-29T00:25:05.801292Z","signed_message":"canonical_sha256_bytes"},"source_id":"2607.25156","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:119617298e451b89f6dbb123b745ddf32aa7503837eefca6e81cc3661f1525a9","sha256:ca39b05eb56e2bc7d691e263cfbe0fd4bb72f3ca948505658d0f637e2f99133c"],"state_sha256":"5515ac9ada64f6236579243eb8573d906e4b082ecaf2459cd717de78d71410f4"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"aUiC2kwy2Wma8sR+Xub16vIXlmTI4DTDG7r9Wf3tNxBzgitp7i+b5g/Z1JHfl6a9PsfVNWITlCBfExJ66CVjAw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-04T22:35:35.211676Z","bundle_sha256":"bc99c0edd525be66710cb53298ec49c12576f0be019cd6065e837d39a23eef08"}}