{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:FTITY4BIX7SQPBLHOMO4A3LVWW","short_pith_number":"pith:FTITY4BI","canonical_record":{"source":{"id":"2607.26397","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CL","submitted_at":"2026-07-29T02:16:09Z","cross_cats_sorted":["cs.LG","q-bio.QM"],"title_canon_sha256":"045fc480ae17bf534961af7cd64cf46b0ad41b36a1a4a66c4167116a72f81ed4","abstract_canon_sha256":"4b6d558e51107974be0a4db039f479096b68a3f6ea4e68a75f1370ac75a4fbb6"},"schema_version":"1.0"},"canonical_sha256":"2cd13c7028bfe5078567731dc06d75b5a8a83657bc96d5ff221ca68a3831f0b0","source":{"kind":"arxiv","id":"2607.26397","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.26397","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"arxiv_version","alias_value":"2607.26397v1","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.26397","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"pith_short_12","alias_value":"FTITY4BIX7SQ","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"pith_short_16","alias_value":"FTITY4BIX7SQPBLH","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"pith_short_8","alias_value":"FTITY4BI","created_at":"2026-07-30T01:18:18Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:FTITY4BIX7SQPBLHOMO4A3LVWW","target":"record","payload":{"canonical_record":{"source":{"id":"2607.26397","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CL","submitted_at":"2026-07-29T02:16:09Z","cross_cats_sorted":["cs.LG","q-bio.QM"],"title_canon_sha256":"045fc480ae17bf534961af7cd64cf46b0ad41b36a1a4a66c4167116a72f81ed4","abstract_canon_sha256":"4b6d558e51107974be0a4db039f479096b68a3f6ea4e68a75f1370ac75a4fbb6"},"schema_version":"1.0"},"canonical_sha256":"2cd13c7028bfe5078567731dc06d75b5a8a83657bc96d5ff221ca68a3831f0b0","receipt":{"kind":"pith_receipt","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"2cd13c7028bfe5078567731dc06d75b5a8a83657bc96d5ff221ca68a3831f0b0","last_reissued_at":"2026-07-30T01:18:18.716492Z","signature_status":"unsigned_v0","first_computed_at":"2026-07-30T01:18:18.716492Z"},"source_kind":"arxiv","source_id":"2607.26397","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":"2026-07-30T01:18:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"ahY1FZTL4hoFaFd6spL3qg8MYGEor1kzM0w1+cbMJ9Bay+OA8hBHAdOrRU4T4QyBouZ7g9MiNCBsHRQ9lhzlCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T10:05:23.467327Z"},"content_sha256":"99ecf9b847d74d6a5cae3ae022e09c4e8d61f353a81b4bb87ca5acc83a7d93f2","schema_version":"1.0","event_id":"sha256:99ecf9b847d74d6a5cae3ae022e09c4e8d61f353a81b4bb87ca5acc83a7d93f2"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:FTITY4BIX7SQPBLHOMO4A3LVWW","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Knowledge before Reasoning: EC-Reason-Bench, a Training-Free Diagnostic Benchmark for LLM Enzyme Classification","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.LG","q-bio.QM"],"primary_cat":"cs.CL","authors_text":"Dongming Jin, Gadeng Luosang, Huanyao Zhang, Linyu Li, Nyima Tashi, Xuan Zhang, Yichi Zhang, Yuanpeng He, Zhi Jin","submitted_at":"2026-07-29T02:16:09Z","abstract_excerpt":"Enzyme function prediction is a hierarchical, knowledge-intensive form of protein function classification. Existing benchmarks expose an anomaly: general LLMs often get the coarse first level right, yet once asked for a complete EC number their accuracy at levels two through four drops to almost zero, while specialized models and tools stay usable. We propose EC-Reason-Bench, a training-free, diagnostic evaluation protocol built to answer two questions: why general LLMs score close to nothing on EC number prediction, and how much of that loss can be recovered without updating a single weight. "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.26397","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/2607.26397/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":"2026-07-30T01:18:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Ac62ayBVENR9N+2yOB0CHAMxIRurcmKlj6a5qgqx/Q/CcdW+hr1LAsFnzP0QzgI8jDT9omi/z7J8A365vKAbCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T10:05:23.467978Z"},"content_sha256":"e4776ebcca392eed16e6666b5aa4c151228678ce1c4c6eeee4bb15bde9195885","schema_version":"1.0","event_id":"sha256:e4776ebcca392eed16e6666b5aa4c151228678ce1c4c6eeee4bb15bde9195885"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/FTITY4BIX7SQPBLHOMO4A3LVWW/bundle.json","state_url":"https://pith.science/pith/FTITY4BIX7SQPBLHOMO4A3LVWW/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/FTITY4BIX7SQPBLHOMO4A3LVWW/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":"2026-08-04T10:05:23Z","links":{"resolver":"https://pith.science/pith/FTITY4BIX7SQPBLHOMO4A3LVWW","bundle":"https://pith.science/pith/FTITY4BIX7SQPBLHOMO4A3LVWW/bundle.json","state":"https://pith.science/pith/FTITY4BIX7SQPBLHOMO4A3LVWW/state.json","well_known_bundle":"https://pith.science/.well-known/pith/FTITY4BIX7SQPBLHOMO4A3LVWW/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:FTITY4BIX7SQPBLHOMO4A3LVWW","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":"4b6d558e51107974be0a4db039f479096b68a3f6ea4e68a75f1370ac75a4fbb6","cross_cats_sorted":["cs.LG","q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CL","submitted_at":"2026-07-29T02:16:09Z","title_canon_sha256":"045fc480ae17bf534961af7cd64cf46b0ad41b36a1a4a66c4167116a72f81ed4"},"schema_version":"1.0","source":{"id":"2607.26397","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2607.26397","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"arxiv_version","alias_value":"2607.26397v1","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2607.26397","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"pith_short_12","alias_value":"FTITY4BIX7SQ","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"pith_short_16","alias_value":"FTITY4BIX7SQPBLH","created_at":"2026-07-30T01:18:18Z"},{"alias_kind":"pith_short_8","alias_value":"FTITY4BI","created_at":"2026-07-30T01:18:18Z"}],"graph_snapshots":[{"event_id":"sha256:e4776ebcca392eed16e6666b5aa4c151228678ce1c4c6eeee4bb15bde9195885","target":"graph","created_at":"2026-07-30T01:18:18Z","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/2607.26397/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Enzyme function prediction is a hierarchical, knowledge-intensive form of protein function classification. Existing benchmarks expose an anomaly: general LLMs often get the coarse first level right, yet once asked for a complete EC number their accuracy at levels two through four drops to almost zero, while specialized models and tools stay usable. We propose EC-Reason-Bench, a training-free, diagnostic evaluation protocol built to answer two questions: why general LLMs score close to nothing on EC number prediction, and how much of that loss can be recovered without updating a single weight. ","authors_text":"Dongming Jin, Gadeng Luosang, Huanyao Zhang, Linyu Li, Nyima Tashi, Xuan Zhang, Yichi Zhang, Yuanpeng He, Zhi Jin","cross_cats":["cs.LG","q-bio.QM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CL","submitted_at":"2026-07-29T02:16:09Z","title":"Knowledge before Reasoning: EC-Reason-Bench, a Training-Free Diagnostic Benchmark for LLM Enzyme Classification"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.26397","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":"sha256:99ecf9b847d74d6a5cae3ae022e09c4e8d61f353a81b4bb87ca5acc83a7d93f2","target":"record","created_at":"2026-07-30T01:18:18Z","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":"4b6d558e51107974be0a4db039f479096b68a3f6ea4e68a75f1370ac75a4fbb6","cross_cats_sorted":["cs.LG","q-bio.QM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"cs.CL","submitted_at":"2026-07-29T02:16:09Z","title_canon_sha256":"045fc480ae17bf534961af7cd64cf46b0ad41b36a1a4a66c4167116a72f81ed4"},"schema_version":"1.0","source":{"id":"2607.26397","kind":"arxiv","version":1}},"canonical_sha256":"2cd13c7028bfe5078567731dc06d75b5a8a83657bc96d5ff221ca68a3831f0b0","receipt":{"builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"2cd13c7028bfe5078567731dc06d75b5a8a83657bc96d5ff221ca68a3831f0b0","first_computed_at":"2026-07-30T01:18:18.716492Z","kind":"pith_receipt","last_reissued_at":"2026-07-30T01:18:18.716492Z","receipt_version":"0.3","signature_status":"unsigned_v0"},"source_id":"2607.26397","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:99ecf9b847d74d6a5cae3ae022e09c4e8d61f353a81b4bb87ca5acc83a7d93f2","sha256:e4776ebcca392eed16e6666b5aa4c151228678ce1c4c6eeee4bb15bde9195885"],"state_sha256":"0f82f88bccc069a40d08f0e551d5918b6ef3e75a764f964dc97b994d6843d191"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"AiR7jSlxZ8FFkcl9ye3Kj79NmyApUt18UfCiqe7GBe/uriiod+fw0aRHI1uRAQvmke+RiU6hZtnOMCc/vp02Dw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-04T10:05:23.475803Z","bundle_sha256":"99cde67cf74ca04fb26bb68326463e7a4b82daf76a5de7a3f5bbe755dcf5922b"}}