{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:HXO6VRVPUHOTHG44L2XMDM7WCK","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":"4a3249ead68f9497c6d36fc1889deeed3a1e70a5da5370840bb399c2b4f41433","cross_cats_sorted":["cs.LG","q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-12T05:36:12Z","title_canon_sha256":"90888e3849d49c9c395911c69e031fbc3e725766e4462e6d63b3c36662840808"},"schema_version":"1.0","source":{"id":"2503.09085","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2503.09085","created_at":"2026-07-05T11:01:32Z"},{"alias_kind":"arxiv_version","alias_value":"2503.09085v2","created_at":"2026-07-05T11:01:32Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2503.09085","created_at":"2026-07-05T11:01:32Z"},{"alias_kind":"pith_short_12","alias_value":"HXO6VRVPUHOT","created_at":"2026-07-05T11:01:32Z"},{"alias_kind":"pith_short_16","alias_value":"HXO6VRVPUHOTHG44","created_at":"2026-07-05T11:01:32Z"},{"alias_kind":"pith_short_8","alias_value":"HXO6VRVP","created_at":"2026-07-05T11:01:32Z"}],"graph_snapshots":[{"event_id":"sha256:0f58c5d80a3c2b081629e0722e84636b13f9541c2bbeff3a360aa16b2123ec43","target":"graph","created_at":"2026-07-05T11:01:32Z","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/2503.09085/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"The Nearest Neighbor model is the $\\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains $\\approx13,000$ underlying thermodynamic parameters, and fitting these to both experimental and structural data is computationally challenging. Here, we leverage recent advances in $\\textit{differentiable folding}$, a method for directly computing gradients of the RNA folding algorithms, to devise an efficient, scalable, and flexible means of parameter optimization ","authors_text":"David H. Mathews, Jeffrey Zuber, Max Ward, Ryan K. Krueger, Sharon Aviran","cross_cats":["cs.LG","q-bio.QM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-12T05:36:12Z","title":"Differentiable Folding for Nearest Neighbor Model Optimization"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2503.09085","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":"sha256:4c653c0e11eb56b8846386d53271de8e083d73ce9ba474dafc290aecd00edc12","target":"record","created_at":"2026-07-05T11:01:32Z","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":"4a3249ead68f9497c6d36fc1889deeed3a1e70a5da5370840bb399c2b4f41433","cross_cats_sorted":["cs.LG","q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-12T05:36:12Z","title_canon_sha256":"90888e3849d49c9c395911c69e031fbc3e725766e4462e6d63b3c36662840808"},"schema_version":"1.0","source":{"id":"2503.09085","kind":"arxiv","version":2}},"canonical_sha256":"3dddeac6afa1dd339b9c5eaec1b3f61298db641606bd72fa6d673a43dbaacb89","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"3dddeac6afa1dd339b9c5eaec1b3f61298db641606bd72fa6d673a43dbaacb89","first_computed_at":"2026-07-05T11:01:32.816058Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T11:01:32.816058Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"zWLHsVEt1fBbD7TL7y1eyqUNo2CavVuVrOQ0NRyyUP/K5u0GfbiBCGafuuQcjCjOigfmGlLBvQ8aNz8zU51tAA==","signature_status":"signed_v1","signed_at":"2026-07-05T11:01:32.816562Z","signed_message":"canonical_sha256_bytes"},"source_id":"2503.09085","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:4c653c0e11eb56b8846386d53271de8e083d73ce9ba474dafc290aecd00edc12","sha256:0f58c5d80a3c2b081629e0722e84636b13f9541c2bbeff3a360aa16b2123ec43"],"state_sha256":"ca7b3c97350597305791f148c5cfa7f0257db3906a291418bac5e417fd922571"}