{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:FVO7JBTTIBAMDK6ZW7RS4KBAZJ","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":"93d8ef9b4b0afefd8c3d850e59f2338183a62b7f07b1620a509b842bccc058ff","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-05T23:04:19Z","title_canon_sha256":"f52c47556a9189623bb425b4fd7b68c7204c7580c0e2e07f70fd14518ff211c1"},"schema_version":"1.0","source":{"id":"2505.03066","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2505.03066","created_at":"2026-07-05T10:58:52Z"},{"alias_kind":"arxiv_version","alias_value":"2505.03066v1","created_at":"2026-07-05T10:58:52Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2505.03066","created_at":"2026-07-05T10:58:52Z"},{"alias_kind":"pith_short_12","alias_value":"FVO7JBTTIBAM","created_at":"2026-07-05T10:58:52Z"},{"alias_kind":"pith_short_16","alias_value":"FVO7JBTTIBAMDK6Z","created_at":"2026-07-05T10:58:52Z"},{"alias_kind":"pith_short_8","alias_value":"FVO7JBTT","created_at":"2026-07-05T10:58:52Z"}],"graph_snapshots":[{"event_id":"sha256:68bb35fdda6a986481cfb22a67bb50cfc0024f6989c685499555f09346f716f1","target":"graph","created_at":"2026-07-05T10:58:52Z","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/2505.03066/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Accurate prediction of enzymatic activity from amino acid sequences could drastically accelerate enzyme engineering for applications such as bioremediation and therapeutics development. In recent years, Protein Language Model (PLM) embeddings have been increasingly leveraged as the input into sequence-to-function models. Here, we use consistently collected catalytic turnover observations for 175 orthologs of the enzyme Adenylate Kinase (ADK) as a test case to assess the use of PLMs and their embeddings in enzyme kinetic prediction tasks. In this study, we show that nonlinear probing of PLM emb","authors_text":"Duncan F. Muir (1), Margaux M. Pinney (1), Michael J. Keiser (1) ((1) University of California, Parker Grosjean (1), San Francisco)","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-05T23:04:19Z","title":"Leveraging Protein Language Model Embeddings for Catalytic Turnover Prediction of Adenylate Kinase Orthologs in a Low-Data Regime"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2505.03066","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:aa2c7c2ea28714f063f7d34235deaaeae2b9f118a24cf8abc9036f26cf59b6d0","target":"record","created_at":"2026-07-05T10:58:52Z","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":"93d8ef9b4b0afefd8c3d850e59f2338183a62b7f07b1620a509b842bccc058ff","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2025-05-05T23:04:19Z","title_canon_sha256":"f52c47556a9189623bb425b4fd7b68c7204c7580c0e2e07f70fd14518ff211c1"},"schema_version":"1.0","source":{"id":"2505.03066","kind":"arxiv","version":1}},"canonical_sha256":"2d5df486734040c1abd9b7e32e2820ca51a50c57ab75c9d3754b729b2ff924dd","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"2d5df486734040c1abd9b7e32e2820ca51a50c57ab75c9d3754b729b2ff924dd","first_computed_at":"2026-07-05T10:58:52.085972Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:58:52.085972Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"ESDJqstCQMRxcvy/ExZYymA+lLMR4nQwPSlEaXcBylXhKWrxf10feQ8YIRfSAyNTCCtU7R09yvWmVV3gjHeJDw==","signature_status":"signed_v1","signed_at":"2026-07-05T10:58:52.086470Z","signed_message":"canonical_sha256_bytes"},"source_id":"2505.03066","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:aa2c7c2ea28714f063f7d34235deaaeae2b9f118a24cf8abc9036f26cf59b6d0","sha256:68bb35fdda6a986481cfb22a67bb50cfc0024f6989c685499555f09346f716f1"],"state_sha256":"c79b3778af2d855afff72a9e907984dd7223c0ff800d9ed835f0b7345bbbc22c"}