Citation audit

Citation Audit

Verify every \cite{...} in a paper against three independent layers:

1. Existence — the cited paper actually exists at the claimed arXiv ID / DOI / venue.
2. Metadata correctness — author names, year, venue, and title match canonical sources (DBLP, arXiv, ACL Anthology, Nature, OpenReview, etc.).
3. Context appropriateness — the cited paper actually supports the claim it is being used to support in the manuscript.

This skill is the fourth layer of \aris{}'s evidence-and-claim assurance, complementing experiment-audit (code), result-to-claim (science verdict), and paper-claim-audit (numerical claims). Together they form a bottom-up integrity stack from raw evaluation code to manuscript bibliography.

When to Use This Skill

Run before submission. The right gating point is:

• After paper-write has produced the LaTeX draft and bib file
• After paper-claim-audit has verified numerical claims
• Before final paper-compile for submission

Do not run this on a half-written draft — most of the work is in cross-checking each \cite against context, which is wasted on placeholder text.

What This Skill Catches

The dangerous citation problems are not wildly fake citations — those are easy to spot. The dangerous ones are:

• Wrong-context citations: real paper, but the cited claim is not what that paper actually establishes (e.g., citing Self-Refine to support "self-feedback produces correlated errors" — Self-Refine actually argues the opposite).
• Author hallucinations: anonymous-author placeholders that slipped through, missing co-authors, wrong order.
• Title drift: arXiv v1 vs v3 with different titles silently merged.
• Venue confusion: arXiv preprint cited but the official venue is now CVPR/ICML/NeurIPS — using the wrong record.
• Year mismatch: arXiv 2023 preprint with 2024 conference acceptance, year reported inconsistently.
• Phantom DOIs: DOI looks real but does not resolve.
• Self-citation drift: your own prior work cited with year off by one.

Constants

• REVIEWER_MODEL = o3 — Used via Codex MCP. Default for cross-model review with web access.
• CONTEXT_POLICY = fresh — Each audit run uses a new reviewer thread (REVIEWER_BIAS_GUARD). Never codex-reply.
• WEB_SEARCH = required — The reviewer must perform real web/DBLP/arXiv lookups, not pattern-match from memory.
• OUTPUT = CITATION_AUDIT.md — Human-readable per-entry verdict report.
• STATE = CITATION_AUDIT.json — Machine-readable verdict ledger consumable by downstream tools.

Workflow

Step 1: Discover bib file and section files

Locate:

• references.bib (or paper.bib / similar) under the paper directory
• All *.tex files containing \cite{...} calls (typically sec/ or sections/)

If multiple bib files exist, audit each separately.

Step 2: Extract all (cite-key, context) pairs

For each \cite{key1,key2,...} invocation in the paper:

• Record the cite key
• Record the file + line number
• Record the surrounding sentence (≥ 1 full sentence around the cite, for context check)

Output a flat list of (key, file, line, surrounding_sentence) tuples.

Also build the inverse: for each bib entry, the list of all places it is cited.

Save the extracted contexts to paper/.aris/citation-audit/contexts.txt so the reviewer can read it directly. Use the paper-dir-relative path .aris/citation-audit/contexts.txt when recording the file in audited_input_hashes; do not stage under /tmp or other transient locations that the verifier cannot rehash later.

Step 3: Send each entry to fresh cross-model reviewer

For each bib entry, invoke mcp__codex__codex (NOT codex-reply — fresh thread per entry, or batch with explicit per-entry isolation):

mcp__codex__codex:
  model: o3
  config: {"model_reasoning_effort": "xhigh"}
  sandbox: read-only
  prompt: |
    You are auditing a bibliographic entry. Use web/DBLP/arXiv search.

    ## Bib entry
    @article{key2024example,
      author = {...}, title = {...}, journal = {...}, year = {...}, ...
    }

    ## Where this entry is cited in the paper
    [paste extracted contexts]

    For this entry, verify:
    1. EXISTENCE: does this paper exist at the claimed arXiv ID / DOI / venue?
       Output: YES / NO / UNCERTAIN, with the verifying URL.
    2. METADATA: are author names, year, venue, title correct?
       For each, output: correct / wrong: should be ... / typo: ...
    3. CONTEXT: for each use, does the cited paper actually support the surrounding claim?
       Output per-use: SUPPORTS / WEAK / WRONG, with one-sentence reasoning.

    VERDICT: KEEP / FIX / REPLACE / REMOVE
    - KEEP: entry is clean, all uses are appropriate
    - FIX: metadata needs correction; uses are appropriate
    - REPLACE: cite is wrong-context, find a different paper that actually supports the claim
    - REMOVE: entry is hallucinated or unsupportable

    Be honest. If you cannot verify online, say UNCERTAIN; do not guess.

Save the response to .aris/traces/citation-audit/<date>_runNN/<key>.md per the review-tracing protocol.

Step 4: Aggregate verdicts

Build CITATION_AUDIT.json following the schema defined in "Submission Artifact Emission" below (single authoritative schema for this file). Per-entry ledger data goes under details.per_entry, not under a top-level entries field. The top-level verdict is a single overall value (PASS / WARN / FAIL / NOT_APPLICABLE / BLOCKED / ERROR) derived from per-entry verdicts per the decision table in "Submission Artifact Emission"; the top-level summary is a one-line human-readable string.

Concretely, details carries the per-entry ledger:

"details": {
  "total_entries": 29,
  "counts": { "KEEP": 11, "FIX": 14, "REPLACE": 3, "REMOVE": 1 },
  "per_entry": [
    {
      "key": "lu2024aiscientist",
      "verdict": "KEEP",
      "axis_failures": [],
      "uses": [
        {"file": "sections/1.intro.tex", "line": 11, "verdict": "SUPPORTS"},
        {"file": "sections/6.related.tex", "line": 8, "verdict": "SUPPORTS"}
      ]
    },
    {
      "key": "madaan2023selfrefine",
      "verdict": "FIX",
      "axis_failures": ["CONTEXT"],
      "uses": [
        {"file": "sections/2.overview.tex", "line": 42, "verdict": "WRONG",
         "note": "Self-Refine demonstrates iterative improvement, not correlated errors"},
        {"file": "sections/6.related.tex", "line": 13, "verdict": "SUPPORTS"}
      ]
    }
  ]
}

See "Submission Artifact Emission" for the full artifact (top-level fields audit_skill, verdict, reason_code, summary, audited_input_hashes, trace_path, thread_id, reviewer_model, reviewer_reasoning, generated_at, details).

Step 5: Generate human-readable report

Write CITATION_AUDIT.md:

# Citation Audit Report

**Date**: 2026-04-19
**Bib file**: references.bib
**Total entries**: 29

## Summary
| Verdict | Count |
|---------|------|
| KEEP    | 11   |
| FIX     | 14   |
| REPLACE | 3    |
| REMOVE  | 1    |

## Priority Fixes (CRITICAL — apply before submission)

### REMOVE: hidden2025aiscientistpitfalls
- Author listed as "Anonymous" — actual authors are Luo, Kasirzadeh, Shah
- Title is incomplete
- ACTION: Replace key with `luo2025aiscientistpitfalls`, update authors and title

### REPLACE-CONTEXT: madaan2023selfrefine in sec/2.overview.tex:42
- Cited to support: "single-model self-refinement can produce correlated errors"
- Self-Refine paper actually demonstrates iterative IMPROVEMENT, not correlated errors
- ACTION: Rewrite the sentence; cite Self-Refine for "self-feedback loop" framing instead

[... continues for each entry ...]

## All-Clean Entries (no action needed)

[list of KEEP keys]

Step 6: Apply fixes (interactive)

For each FIX/REPLACE/REMOVE verdict, prompt the user:

Fix [key]?
  Change: <description of change>
  Files affected: references.bib + sec/X.tex:Y
[Apply / Skip / Defer]

If AUTO_APPLY = true, apply all FIX-level changes (metadata corrections only). REPLACE and REMOVE always require human approval — they involve content changes.

Step 7: Recompile and verify

latexmk -C && latexmk -pdf -interaction=nonstopmode main.tex

Confirm:

• No new Citation undefined warnings
• No Reference undefined warnings
• Page count unchanged or only minimally affected by metadata fixes

Key Rules

• Fresh reviewer thread per audit run — never reuse prior review context
• Web access required — the reviewer must do real lookups, not memory pattern-match
• Wrong-context > metadata — a real paper used to support a wrong claim is more dangerous than a typo in author name
• REPLACE/REMOVE require human approval — never auto-modify content claims
• Always emit, never block — this skill always writes CITATION_AUDIT.json with a verdict; the decision to block finalization lives in paper-writing Phase 6 + tools/verify_paper_audits.sh, driven by the assurance level. See "Submission Artifact Emission" below.
• Run once per submission — the audit is wall-clock expensive (web lookups for each entry); not for every save

Comparison with Other Audit Skills

Skill	What it audits	What it catches
/experiment-audit	Evaluation code	Fake ground truth, self-normalized scores, phantom results
/result-to-claim	Result-to-claim mapping	Claims unsupported by evidence
/paper-claim-audit	Numerical claims in manuscript	Number inflation, best-seed cherry-pick, config mismatch
/citation-audit	Bibliographic entries	Hallucinated refs, wrong-context citations, metadata errors

Together: code → result → numerical claim → cited claim. Each layer has cross-family review with no executor in the validator path.

Known Limitations

• DBLP coverage gap: very recent papers (< 2 weeks) may not yet be in DBLP. Reviewer should fall back to arXiv.
• Pre-print vs published: when both exist, reviewer should prefer the published venue (ICML 2024 over arXiv 2401.xxxxx) but flag both.
• Anthology vs OpenReview: NeurIPS/ICLR papers have OpenReview entries before official proceedings; both are valid sources.
• Multi-author truncation: bib entries with 6+ authors using and others are conventional and not flagged unless the truncation hides a co-author the user explicitly cares about.

Review Tracing

After each mcp__codex__codex reviewer call, save the trace following shared-references/review-tracing.md. Use tools/save_trace.sh or write files directly to .aris/traces/citation-audit/<date>_run<NN>/. Respect the --- trace: parameter (default: full).

Output Contract

• CITATION_AUDIT.md (human-readable report) at paper root
• CITATION_AUDIT.json (machine-readable ledger; schema below) at paper root
• .aris/traces/citation-audit/<date>_runNN/ (per-entry review traces)
• Optional: applied fixes to references.bib + sec/*.tex (with --apply flag)

Submission Artifact Emission

This skill always writes paper/CITATION_AUDIT.json, regardless of caller or detector outcome. A paper with no .bib file or no \cite{...} usage emits verdict NOT_APPLICABLE; silent skip is forbidden. paper-writing Phase 6 and tools/verify_paper_audits.sh both rely on this artifact existing at a predictable path.

The artifact conforms to the schema in shared-references/assurance-contract.md:

{
  "audit_skill":      "citation-audit",
  "verdict":          "PASS | WARN | FAIL | NOT_APPLICABLE | BLOCKED | ERROR",
  "reason_code":      "all_entries_keep | metadata_drift | wrong_context | hallucinated | ...",
  "summary":          "One-line human-readable verdict summary.",
  "audited_input_hashes": {
    "references.bib":             "sha256:...",
    "main.tex":                   "sha256:...",
    "sections/3.related.tex":     "sha256:..."
  },
  "trace_path":       ".aris/traces/citation-audit/<date>_run<NN>/",
  "thread_id":        "<codex mcp thread id>",
  "reviewer_model":   "o3",
  "reviewer_reasoning": "xhigh",
  "generated_at":     "<UTC ISO-8601>",
  "details": {
    "total_entries":  <int>,
    "per_entry":      [ { "key": "madaan2023selfrefine",
                          "verdict": "KEEP | FIX | REPLACE | REMOVE",
                          "axis_failures": [ "CONTEXT" | "METADATA" | "EXISTENCE" ],
                          "note": "..." }, ... ]
  }
}

audited_input_hashes scope

Hash the declared input set actually passed to this audit: the .bib file, main.tex, and every sections/*.tex file that supplied citation contexts. Do NOT hash extracted contexts from /tmp or other transient paths — if you need to stage extracted contexts, materialize them under paper/.aris/ so the verifier can rehash reproducibly. Do NOT hash repo-wide unions or the reviewer's self-reported opened subset.

Path convention (must match tools/verify_paper_audits.sh): keys are paths relative to the paper directory (no paper/ prefix — the verifier already resolves relative to the paper dir; prefixing produces paper/paper/... and false-fails as STALE). Use absolute paths for any file outside the paper dir.

Verdict decision table

Input state	Verdict	reason_code example
No .bib file or no \cite{...} usage	NOT_APPLICABLE	no_citations
.bib file referenced but unreadable / missing	BLOCKED	bib_unreadable
Every entry KEEP, all three axes green	PASS	all_entries_keep
Only FIX verdicts (metadata drift, no context errors)	WARN	metadata_drift
Any REPLACE or REMOVE (wrong-context or hallucinated entry)	FAIL	wrong_context
Web lookups timed out / reviewer invocation failed	ERROR	reviewer_error

Thread independence

Every invocation uses a fresh mcp__codex__codex thread. Never codex-reply. Do not accept prior audit outputs (PROOF_AUDIT, PAPER_CLAIM_AUDIT, EXPERIMENT_LOG) as input — the fresh thread preserves reviewer independence per shared-references/reviewer-independence.md.

This skill never blocks by itself; paper-writing Phase 6 plus the verifier decide whether the verdict blocks finalization based on the assurance level.

See Also

• /paper-claim-audit — sibling skill for numerical claim verification
• /experiment-audit — sibling skill for evaluation code integrity
• /result-to-claim — claim verdict assignment from results
• shared-references/citation-discipline.md — protocol document for citation hygiene
• shared-references/reviewer-independence.md — cross-model review constraints