{"paper":{"id":"2609.00065.pdf","title":"Scientific Agent Skills: A Library of Procedural Knowledge for Research Agents","authors":["Timothy Kassis","Vinayak Agarwal","Yuhuan He","Darshil Patel","Aubrey M. Brueckner"],"arxiv_id":"","url":"","source_kind":"pdf","ir_version":"1.0"},"generated_at":"2026-09-14T04:17:30.212646+00:00","counts":{"error":0,"warning":0,"info":0},"findings":[],"top_findings":[],"ir_summary":{"claims":25,"contributions":5,"method_components":11,"experiments":4,"baselines":0,"datasets":1,"metrics":1,"tables":2,"figures":5,"citations":56,"equations":0,"quantitative_results":139,"has_repository":false},"ir_health":{"observations":[{"code":"compile-warning","severity":"note","message":"semantic extraction: dropped 5 items whose quote was not found in the paper","detail":""}],"errors":0,"warnings":0,"trustworthy":true},"diagnostics":{"source":"/home/oceann/workspace/research-linter/eval/papers/2609.00065.pdf","rules_run":["RL001","RL002","RL003","RL004","RL005"],"rules_skipped":[],"rule_errors":{},"rule_findings":{"RL001":0,"RL002":0,"RL003":0,"RL004":0,"RL005":0},"rule_seconds":{"RL001":0.0,"RL002":129.74,"RL003":5.85,"RL004":0.04,"RL005":0.25},"dropped_no_evidence":0,"demoted_low_confidence":0,"ir_health":{"observations":[{"code":"compile-warning","severity":"note","message":"semantic extraction: dropped 5 items whose quote was not found in the paper","detail":""}],"errors":0,"warnings":0,"trustworthy":true},"notes":["RL001 funnel arithmetic: sentences_with_from=0 endpoint_pairs=0 claims_compared=0 emitted=0 [dropped: not-a-measurement=0]  <- no 'from A to B' sentence reached this check","RL001 funnel delta-column: structured_tables=2 with_exactly_one_delta_column=0 rows_checked=0 emitted=0","RL001 funnel cross-location: quant=139 prose=35 prose_with_metric=1 prose_with_dataset=0 prose_with_metric_and_dataset=0 distinct_buckets=0 emitted=0 [dropped: not-a-measurement=7 not-in-quote=0]","RL001 funnel identifier-drift: settings_checked=2 sections_stating_one_value=0 emitted=0","RL002 citation entailment: attempted 18 of 54 ranked cited claims (117 in-text markers from 56 bibliography entries); 3 cited works could not be identified, 4 had no retrievable text, 0 model quotes failed verbatim verification, 0 were topically unrelated to the retrieved text.","RL002 candidate ranking (why the top 18 were chosen): [6] [introduction, absolutist wording]; [10] [introduction, names an artefact (Agent Skills), unusable title (identity fragile)]; [11] [introduction, names an artefact (Scientific Agent Skills), unusable title (identity fragile)]; [7] [introduction, names an artefact (ARRIVE)]; [8] [introduction, names an artefact (MIQE)]; [18] [introduction, title/sentence overlap near zero, unusable title (identity fragile)]; [1] [introduction, title/sentence overlap near zero]; [5] [introduction, title/sentence overlap near zero]","RL002 label distribution over 11 classified citations: SUPPORTED=11","RL002 base-rate self-check: not tripped (0/11 = 0% NOT_SUPPORTED, threshold 40%).","RL002 attribution check (case B): 9 candidates name an artefact, 4 of them made the top-N and were checked against their cited source","RL002: 4 citations skipped because the sentence reports this paper's own results (the citation there is a comparison pointer, not evidence for the sentence)","RL002: 2 markers skipped because the claim is jointly attributed to several works","RL002: 4 enumerated-citation sentences skipped (they cite >=3 works, so the claim is about the set and cannot be refuted by any single cited work)","RL002: 3 duplicate candidates dropped (same reference and claim, or the same artefact attributed twice)","RL002: 3 cited works unresolvable (first 3: [{\"key\": \"[10]\", \"title\": \"Agent skills specification\", \"why\": \"bibliography title unusable for identity verification\"}, {\"key\": \"[11]\", \"title\": \"Scientific agent skills\", \"why\": \"bibliography title unusable for identity verification\"}, {\"key\": \"[18]\", \"title\": \"Ziru Chen, Shijie Chen, Yuting Ning, Qianheng Zhang, Boshi Wang, Botao Yu, Yifei Li, Zeyi Liao, Chen Wei, Zitong Lu, Vis\", \"why\": \"bibli)","RL003: 2 queries -> 100 unique works (arXiv search 50, category listings 0, scholarly graph 50 [crossref 50], 0 graph works matched to an arXiv id); source errors during retrieval: arXiv 0, graph 0","RL003: parsed the reference list of 1/3 comparable papers (2 unreadable) — that is the PeerUsage denominator","RL003: could read the reference list of only 1 comparable papers (need 4) — peer usage unavailable, no findings","RL004 funnel: components=11 contribution_backed=1 candidates=0 ablations_found=0 matched_by_ablation=0 unmatched=0 experiments=4","RL004 component M1 'skill directory': excluded:not-a-claimed-contribution","RL004 component M2 'SKILL.md': covered (filtered earlier)","RL004 component M3 'name, description, license, compatibility, allowed-tools and metadata': excluded:not-a-claimed-contribution","RL004 component M4 'references/ for additional documentation, scripts/ for code, and assets/ for templates and static resources': excluded:not-a-claimed-contribution","RL004 component M5 'progressive disclosure': excluded:not-a-claimed-contribution","RL004 component M6 'three-tier disclosure model': excluded:not-a-claimed-contribution","RL004 component M7 'cross-references': excluded:evaluation-infrastructure-or-packaging","RL004 component M8 'bag of lower-cased alphanumeric tokens that are at least 3 characters long': covered (filtered earlier)","RL004 component M9 '500-line limit on instruction files': excluded:not-a-claimed-contribution","RL004 component M10 'throwaway environment per skill': excluded:not-a-claimed-contribution","RL004 component M11 'tests outside the shipped directory': excluded:not-a-claimed-contribution","RL004 funnel: ranked=0 emitted=0 suppressed_by_cap=0 dropped_unverified_quote=0","RL005: repository read, but the paper states no comparable hyperparameter"],"missing_core_rules":[],"seconds":151.16,"llm":{"calls":11,"cache_hits":2,"errors":0,"prompt_chars":83407},"sources":{"arxiv":{"requests":23,"errors":0,"cache_hits":17,"available":1},"openalex":{"requests":1,"errors":0,"cache_hits":0,"available":0,"unavailable_reason":"OpenAlex free daily budget exhausted (resets midnight UTC)"},"crossref":{"requests":17,"errors":0,"cache_hits":1,"available":1},"s2":{"requests":0,"errors":0,"cache_hits":0,"available":1},"short_circuited":["crossref","openalex","s2"]},"cache":{"hits":20,"misses":52}},"compile_warnings":["semantic extraction: dropped 5 items whose quote was not found in the paper"]}