{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:YHYHD6XA5VZOCYKUXIKDVJY25N","short_pith_number":"pith:YHYHD6XA","canonical_record":{"source":{"id":"2507.15912","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-07-21T16:41:58Z","cross_cats_sorted":[],"title_canon_sha256":"88a776ae399ebdc6ede910309a6479711a4a53b719a10a4c56e5b16c63a3ee50","abstract_canon_sha256":"993198e6cf9d3d3da3368399acf03835f6cae28a9b8191198880e9b3b9cd5002"},"schema_version":"1.0"},"canonical_sha256":"c1f071fae0ed72e16154ba143aa71aeb4cd8373d870835847bde5f40102c3f9d","source":{"kind":"arxiv","id":"2507.15912","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2507.15912","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"arxiv_version","alias_value":"2507.15912v1","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2507.15912","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"pith_short_12","alias_value":"YHYHD6XA5VZO","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"pith_short_16","alias_value":"YHYHD6XA5VZOCYKU","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"pith_short_8","alias_value":"YHYHD6XA","created_at":"2026-07-05T11:40:59Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:YHYHD6XA5VZOCYKUXIKDVJY25N","target":"record","payload":{"canonical_record":{"source":{"id":"2507.15912","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-07-21T16:41:58Z","cross_cats_sorted":[],"title_canon_sha256":"88a776ae399ebdc6ede910309a6479711a4a53b719a10a4c56e5b16c63a3ee50","abstract_canon_sha256":"993198e6cf9d3d3da3368399acf03835f6cae28a9b8191198880e9b3b9cd5002"},"schema_version":"1.0"},"canonical_sha256":"c1f071fae0ed72e16154ba143aa71aeb4cd8373d870835847bde5f40102c3f9d","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T11:40:59.149746Z","signature_b64":"oxP/BGK1FUO/UJCMISEncSZi3Cbbv2DQjPDRJUlg4sxo1mI94VgMrxtnLYaJ3UVcXnl3QCKRoZCDXKSuWMeYCw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"c1f071fae0ed72e16154ba143aa71aeb4cd8373d870835847bde5f40102c3f9d","last_reissued_at":"2026-07-05T11:40:59.149240Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T11:40:59.149240Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2507.15912","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":"2026-07-05T11:40:59Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"YcuJHHsUzPcXwBJITNL/L2mifUf3yWBNSvZmV8zZh1smvuSEZXivO1ExHVC4eJEdUhZR0Shmp4bwuPVxFPpSDQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-19T11:40:23.598348Z"},"content_sha256":"af293b4679515fe0ef830c902c21e809d15c7362846997213439e01f8d3d810a","schema_version":"1.0","event_id":"sha256:af293b4679515fe0ef830c902c21e809d15c7362846997213439e01f8d3d810a"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:YHYHD6XA5VZOCYKUXIKDVJY25N","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Efficient design of rna sequences with desired properties, structure, and motifs using a grammar variational autoencoder","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.QM","authors_text":"Byung-Jun Yoon, Narges Zarnaghinaghsh","submitted_at":"2025-07-21T16:41:58Z","abstract_excerpt":"Designing structurally stable RNA sequences with specific motifs and other desirable properties is an important challenge in bioinformatics. The potential design space increases exponentially with the length of the RNA to be engineered, which makes this a difficult combinatorial optimization problem. In this paper, we propose an RNA grammar variational autoencoder (RGVAE) that can efficiently generate novel RNA sequences with specific target properties. The proposed RGVAE builds on the recently proposed grammar VAE, where we incorporate the stochastic context-free grammar (SCFG) to design stru"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2507.15912","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/2507.15912/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":"2026-07-05T11:40:59Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"gTo6zueA2PaCTY/TIqYaaMXD28Sl+FW3TZCuXeJCSmjBmciruhKytEe0uXZZ3Pa8lALcEO4VExuxMUqxSsI6BQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-19T11:40:23.599699Z"},"content_sha256":"a157fd4436027a8cf10ab682cce68a2ad2cc6c114b46ea08d3611f2b93da89ba","schema_version":"1.0","event_id":"sha256:a157fd4436027a8cf10ab682cce68a2ad2cc6c114b46ea08d3611f2b93da89ba"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/YHYHD6XA5VZOCYKUXIKDVJY25N/bundle.json","state_url":"https://pith.science/pith/YHYHD6XA5VZOCYKUXIKDVJY25N/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/YHYHD6XA5VZOCYKUXIKDVJY25N/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":"2026-08-19T11:40:23Z","links":{"resolver":"https://pith.science/pith/YHYHD6XA5VZOCYKUXIKDVJY25N","bundle":"https://pith.science/pith/YHYHD6XA5VZOCYKUXIKDVJY25N/bundle.json","state":"https://pith.science/pith/YHYHD6XA5VZOCYKUXIKDVJY25N/state.json","well_known_bundle":"https://pith.science/.well-known/pith/YHYHD6XA5VZOCYKUXIKDVJY25N/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:YHYHD6XA5VZOCYKUXIKDVJY25N","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":"993198e6cf9d3d3da3368399acf03835f6cae28a9b8191198880e9b3b9cd5002","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-07-21T16:41:58Z","title_canon_sha256":"88a776ae399ebdc6ede910309a6479711a4a53b719a10a4c56e5b16c63a3ee50"},"schema_version":"1.0","source":{"id":"2507.15912","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2507.15912","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"arxiv_version","alias_value":"2507.15912v1","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2507.15912","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"pith_short_12","alias_value":"YHYHD6XA5VZO","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"pith_short_16","alias_value":"YHYHD6XA5VZOCYKU","created_at":"2026-07-05T11:40:59Z"},{"alias_kind":"pith_short_8","alias_value":"YHYHD6XA","created_at":"2026-07-05T11:40:59Z"}],"graph_snapshots":[{"event_id":"sha256:a157fd4436027a8cf10ab682cce68a2ad2cc6c114b46ea08d3611f2b93da89ba","target":"graph","created_at":"2026-07-05T11:40:59Z","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/2507.15912/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Designing structurally stable RNA sequences with specific motifs and other desirable properties is an important challenge in bioinformatics. The potential design space increases exponentially with the length of the RNA to be engineered, which makes this a difficult combinatorial optimization problem. In this paper, we propose an RNA grammar variational autoencoder (RGVAE) that can efficiently generate novel RNA sequences with specific target properties. The proposed RGVAE builds on the recently proposed grammar VAE, where we incorporate the stochastic context-free grammar (SCFG) to design stru","authors_text":"Byung-Jun Yoon, Narges Zarnaghinaghsh","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-07-21T16:41:58Z","title":"Efficient design of rna sequences with desired properties, structure, and motifs using a grammar variational autoencoder"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2507.15912","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:af293b4679515fe0ef830c902c21e809d15c7362846997213439e01f8d3d810a","target":"record","created_at":"2026-07-05T11:40:59Z","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":"993198e6cf9d3d3da3368399acf03835f6cae28a9b8191198880e9b3b9cd5002","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-07-21T16:41:58Z","title_canon_sha256":"88a776ae399ebdc6ede910309a6479711a4a53b719a10a4c56e5b16c63a3ee50"},"schema_version":"1.0","source":{"id":"2507.15912","kind":"arxiv","version":1}},"canonical_sha256":"c1f071fae0ed72e16154ba143aa71aeb4cd8373d870835847bde5f40102c3f9d","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"c1f071fae0ed72e16154ba143aa71aeb4cd8373d870835847bde5f40102c3f9d","first_computed_at":"2026-07-05T11:40:59.149240Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T11:40:59.149240Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"oxP/BGK1FUO/UJCMISEncSZi3Cbbv2DQjPDRJUlg4sxo1mI94VgMrxtnLYaJ3UVcXnl3QCKRoZCDXKSuWMeYCw==","signature_status":"signed_v1","signed_at":"2026-07-05T11:40:59.149746Z","signed_message":"canonical_sha256_bytes"},"source_id":"2507.15912","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:af293b4679515fe0ef830c902c21e809d15c7362846997213439e01f8d3d810a","sha256:a157fd4436027a8cf10ab682cce68a2ad2cc6c114b46ea08d3611f2b93da89ba"],"state_sha256":"3feb6b250ebafad53117a97a856925a172173bd2b6f564033b0165303b2a43d9"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"midy+in+Skyu87nq56TUsJun2QpXzrfjUge5Ho6WcJZjTRGwbLZqRXVrHoXYS4bNn1dLYS57GfmqNEA7rcaHDQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-19T11:40:23.606861Z","bundle_sha256":"47727f2d13299226f97010c5a149bf24f0b045ac9c8d6ffe0305a3d5af1b455d"}}