/academic-paper

Policy-Anchor Disclosure Protocol

Status: #108 implementation (parented to Decision Doc 20ed72d) Parent skill: academic-paper Mode name: disclosure with --policy-anchor=<a> selector (parallel track to --venue=<v> v3.2 path; see disclosure_mode_protocol.md for the dispatch). Anchor inventory: prisma-trAIce, icmje, nature, ieee (closed enum; expansion via §4.7 deferred per Decision Doc §4.2). Data source: policy_anchor_table.md (read at runtime; LLM looks up the row for --policy-anchor=<a> × field-N).

This protocol document is the runtime instruction set the LLM follows when the user invokes disclosure mode with a policy-anchor selector. It encodes the 8 Decision Doc §4.3 frozen invariants, the §3 G10 7-row precedence table for whole-disclosure output decision, the 11 §4.4 open-concern resolutions (per implementation spec §3), the auto-promotion forbiddance, and the per-anchor render flows (PRISMA-trAIce / ICMJE / Nature / IEEE).

0. Why this protocol exists

ARS's v3.2 disclosure mode renders a venue-targeted applicability/status bundle (REQUIRED, ACTION_ONLY, NOT_REQUIRED, or UNKNOWN, plus typed fail-closed halt status; 15 policy targets as of the v2 database: ICLR, NeurIPS, Nature, Science, ACL, EMNLP, plus the #596 medical-publishing set — see venue_disclosure_policies.md). The 4-anchor --policy-anchor=<a> track instead uses the anchor-specific output contract below when the author targets a policy anchor (PRISMA-trAIce, ICMJE, Nature Portfolio, IEEE) rather than a specific journal venue. The two tracks coexist; v3.2 venue path remains the default for journal submissions.

1. Inputs

1. Paper draft (same as v3.2): manuscript text plus pipeline log if available.
2. Selector: --policy-anchor=<a> where a ∈ {prisma-trAIce, icmje, nature, ieee}. Selector-mutually-exclusive by default — supplying both --policy-anchor and --venue triggers the §5 conflict-resolution flow, which permits exactly one consistent pair (any Nature Portfolio venue + --policy-anchor=nature, sharing the canonical shared/policy_data/nature_policy.md source) and rejects every other combination with explicit error. See §5 for the full enumeration.
3. Pipeline signal: slr_lineage=true|false set by the upstream pipeline orchestrator when an SLR-mode stage appears in the run history. Drives the §4.3 G2 invariant track gate (concern #1 resolution: explicit slr_lineage input).
4. Cold-start fallback: when the renderer runs outside a pipeline (no slr_lineage set), the author supplies mode=<value> explicitly. Silent fallback to general track on missing input is forbidden by §4.3 G2 invariant.
5. v3.2 Phase 2 AI usage categorization: the same input shape v3.2 uses. Each AI usage category carries state ∈ {USED, NOT USED, UNCERTAIN}.
6. Optional ai_used: true | false: explicit author-supplied flag layered on top of category state. Composes with category state per §2 G10 7-row precedence table below.
7. Tool identity per AI tool (concern #2 resolution): auto-detected from session metadata (mirror v3.2 disclosure_mode_protocol.md Phase 4 detection); explicit fallback per tool when session metadata absent or non-Claude tools are involved.

2. Whole-disclosure decision — §3 G10 7-row precedence table

Rows are evaluated in priority order from top to bottom; the renderer emits the output of the first row whose precondition matches. Subsequent rows do not fire. This table is the §4.3 G3 / G10 invariant in load-bearing form.

Before evaluating this table, apply the shared Phase-2 intake-integrity gate in disclosure_mode_protocol.md: a USED OTHER / UNCLASSIFIED category halts until the author maps it to an executable category. Row 4 cannot render from an unclassified-use record; emit an honest "AI-disclosure intake incomplete — unclassified use requires author mapping" annotation instead. The same intake-pending annotation applies when the shared external-use inventory is not author-confirmed.

Concern #10 resolution (ai_used: true substantive-content gate): when ai_used: true is supplied and no v3.2 category is marked USED (regardless of whether Phase 2 has been performed — i.e., this gate fires for both "bare-flag input only, no categorization" and "Phase 2 done but every category came back NOT USED while ai_used:true is still set"), row 4 does not emit a complete render. Instead, the input is treated as a prompt-trigger that halts the current run and asks the user to reconcile: either supply a USED category, change ai_used to false, or run / re-run v3.2 Phase 2 categorization. Once a USED category is supplied (or ai_used flipped), re-evaluate against the §2 table from the top. This implements the concern #10 resolved path: "force v3.2 categorization flow", consistent with concern #6's honest-signal-preservation discipline. The forbiddance: emitting a full anchor disclosure with ai_used:true and zero USED facets.

3. Per-anchor render flows

For each anchor, the renderer reads policy_anchor_table.md rows 1..16 and applies the field-level rules below. The 4 anchors share the row-4 dispatcher above; the per-anchor sections only describe what to emit after row 4 fires.

3.1 --policy-anchor=prisma-trAIce

Track gate (G2 invariant): this anchor is only valid when slr_lineage=true (pipeline signal) or mode=systematic-review (cold-start input). Selecting --policy-anchor=prisma-trAIce with slr_lineage=false is non-conformant — the renderer refuses with an explicit error citing the G2 invariant.

G5 invariant — three gates for M6 prompt disclosure: PRISMA-trAIce M6 prompt disclosure fires only when all three hold:

1. PRISMA-trAIce track selected (the gate above).
2. tool_type ∈ {LLM, GenAI} (per PRISMA M6 "if any" predicate).
3. AI use is methodological-in-SLR (search / screening / data extraction / Risk of Bias / synthesis / drafting per PRISMA M3.a), not pure copyediting.

When gate 3 fails (SLR manuscript whose only LLM use is editorial), the renderer routes to the §3.5 copyediting-carve-out path instead. PRISMA-trAIce track does not own the copyediting case.

Render fields:

• Per policy_anchor_table.md row 1–3: emit one tool identity tuple per AI tool (concern #2 resolution; auto-detect from session, fallback explicit). Identity tuple = (tool name, version if applicable, developer/provider).
• Row 4–5: emit one (tool × task) record per (tool, task) tuple across the M3.a 6-stage enum (concern #3 resolution). Missing tuples produce "not supplied" annotation per tuple. Per-task prompt disclosure follows M6.a granularity.
• Row 8: emit prompt records per (tool × task) tuple per gate G5.
• Row 9: emit human oversight description per M8 sub-items.
• Rows 11–12: emit performance evaluation method + results per M9 + R2 when applicable.
• Row 13: emit limitations narrative per D1.
• Row 14: distribute disclosure fragments per Table 1 row groupings (Title / Abstract / Introduction / Methods / Results / Discussion). The renderer emits per-section fragments, not a single paragraph.

3.2 --policy-anchor=icmje

Track gate: no SLR lineage requirement. Available regardless of slr_lineage value.

Render fields:

• Row 10 (explicit-mandate): emit ICMJE human-responsibility statement using the verbatim "humans are responsible for any submitted material that included the use of AI-assisted technologies" language. This sentence appears in every ICMJE render where row 4 fires.
• Row 14 (explicit-recommend): emit two channels — cover letter (verbatim ICMJE language) + manuscript "appropriate section" (per the venue's submission policy). The two channels carry different paragraphs, not a single duplicated paragraph.
• Row 16 (explicit-mandate): emit the text-attribution clause: appropriate attribution and full citations for AI-quoted material + the prohibition against citing AI-generated material as primary source. Surface this paragraph even when no images are involved (rule covers text-attribution).
• Rows with not-addressed strength (9/16 cells): the renderer skips these by default; if v3.2 Phase 2 provides a category USED that would be served by such a field, surface a "ICMJE delegates this detail to journal-level policy; consider the v3.2 venue track for journal-specific phrasing" annotation.

3.3 --policy-anchor=nature

Track gate: no SLR lineage requirement.

Dedup with v3.2 Nature venue path: the Nature substantive policy text is co-cited from shared/policy_data/nature_policy.md (canonical source pointer). Both consumers — the v3.2 Nature venue renderer in venue_disclosure_policies.md and this Nature anchor renderer — derive their substantive content from that shared source. G4 invariant: edits to Nature-specific policy quotes must go through the shared source first, never directly into either consumer.

Render fields:

• Rows 9–10 (both explicit-mandate): emit the human-accountability statement using Nature's "In all cases, there must be human accountability for the final version of the text" verbatim language. Combine with the authorship-rejection clause from row 10's second quote when the manuscript proposes any AI co-authorship.
• Row 14 (explicit-recommend): emit Methods-section placement instruction citing the verbatim "Methods section (and if a Methods section is not available, in a suitable alternative part)" language.
• Row 15 (explicit-recommend) carve-out semantics: eliminate strength. Copyediting-only use produces no disclosure paragraph, only an internal renderer log entry. The §4.3 G7 invariant forbids collapsing this into a boolean shared with IEEE's downgrade semantics.
• Row 16 (explicit-mandate) image-rights handling: concern #5 resolution = hybrid (annotation block + suggested inline patches). The renderer emits two outputs:
  1. A standalone image_disclosure_instructions.md block describing, per image, which Nature carve-out applies (or default-deny) and what Nature label text appears in the image field.
  2. A suggested patch diff against manuscript source figure metadata (caption, alt-text, image-field caption) for the author to optionally apply. ARS does not modify manuscript source autonomously; the patch is suggested-only.

3.4 --policy-anchor=ieee

Track gate: no SLR lineage requirement.

G8 invariant — paired mandate: IEEE row 5 (Specific task within stage, explicit-mandate) and row 6 (Affected manuscript sections / content locator, explicit-mandate) are a paired mandate. The renderer emits both inputs together. Emitting level_of_involvement (row 5 narrative annotation) without an affected_sections locator (row 6) — or vice versa — is non-conformant.

Concern #4 resolution (IEEE section locator shape): free-form list with recommended IMRaD exemplars. Accepted values: "Introduction" | "Methods" | "Results" | "Discussion" | "Abstract" | "Title" | free-form-other. Closed-enum would over-constrain IEEE's "brief explanation" language; free-form preserves the policy's narrative invitation. Test fixture covers both exemplar-match and free-form-other inputs.

Render fields:

• Row 1 (explicit-mandate): emit "The AI system used shall be identified" formulation — name + identifier per AI tool.
• Rows 5–6 (paired explicit-mandate per G8): emit affected_sections list + level_of_involvement narrative annotation together.
• Row 14 (explicit-mandate): emit placement instruction citing "acknowledgments section of any article submitted to an IEEE publication" verbatim. No Methods placement, no cover-letter channel — the tightest closed enum across all four anchors.
• Row 15 (explicit-recommend) carve-out semantics: downgrade-not-eliminate strength. Copyediting-only use still produces a disclosure paragraph at the same acknowledgments location, but with recommend-strength rather than mandate language. The §4.3 G7 invariant forbids collapsing this into a boolean shared with Nature's eliminate semantics.
• Row 16 (implicit): images/figures/code fold into the same acknowledgments-disclosure mandate as text. No separate image-rights regime, no default-prohibition (contrasts with Nature). The renderer emits a single acknowledgments paragraph covering all content types per IEEE policy. The §4.3 G9 invariant: each anchor's image-rights regime stays distinct; IEEE's fold-into-acknowledgments path does not merge with Nature's default-deny regime.

3.5 Copyediting carve-out cross-anchor handling

Per §4.3 G7 invariant + §4.5 / §4.6 cell #15, the copyediting carve-out semantics are anchor-specific:

• Nature anchor: eliminate strength — no disclosure paragraph for copyediting-only use.
• IEEE anchor: downgrade-not-eliminate — disclosure still emitted at acknowledgments, with recommend-strength language ("is recommended" rather than "shall be disclosed").
• PRISMA-trAIce anchor: not in scope (M6 G5 gate 3 routes copyediting cases away from PRISMA-trAIce track entirely; see §3.1).
• ICMJE anchor: not-addressed in the policy text; the renderer treats copyediting cases per the same path as substantive AI use (no carve-out, full ICMJE render).

The renderer MUST NOT collapse these four behaviors into a single boolean exempted_uses: [copyediting] field — doing so would silently lose the eliminate-vs-downgrade-vs-not-in-scope distinctions.

4. Auto-promotion forbiddance (§4.3 G3 / G10 invariant)

A still-UNCERTAIN category MUST NOT be rendered as though USED in any of the four anchor outputs. This is the load-bearing constraint behind concern #6's resolution: USED facets render at full strength; UNCERTAIN facets surface the per-facet annotation, never the full-strength render. The renderer MUST surface UNCERTAIN as UNCERTAIN throughout the disclosure text; silent promotion of any UNCERTAIN category to USED is forbidden.

The test suite covers this forbiddance with negative fixtures asserting that an input with ai_used:true + 1 UNCERTAIN category + 0 USED categories does NOT emit a full-strength render of the UNCERTAIN category.

5. Venue + anchor conflict resolution (concern #7)

When the user passes both --venue=<v> and --policy-anchor=<a>, the renderer evaluates whether the two map to compatible policies. The consistent-pair recognition for the Nature track covers the full Nature Portfolio venue family:

• Consistent — Nature Portfolio venue + --policy-anchor=nature: includes canonical labels {"Nature", "Nature Portfolio", "Nature (Nature Publishing Group)", "Nature Publishing Group"} and any venue whose name starts with the prefix "Nature " (e.g., Nature Medicine, Nature Communications, Nature Climate Change, Nature Energy, Nature Methods, ...). All Nature Portfolio journals inherit the same parent AI policy, so each of these venue strings + --policy-anchor=nature proceeds via the shared source pointer.
• Conflicting — any other (venue, anchor) pair: e.g., --venue=Nature + --policy-anchor=IEEE, --venue=ICLR + --policy-anchor=icmje, or a Nature Portfolio venue with a non-nature anchor → reject with explicit error listing the policy conflict and the canonical Nature consistent-pair definition above.

Silent precedence is forbidden (Decision Doc §4.4 #7 + concern #7 resolution). The renderer must surface the conflict to the user and require an explicit selector choice. The recognition logic above is mirrored by the conformance referee's is_nature_portfolio_venue() helper in scripts/policy_anchor_disclosure_referee.py — when this protocol text drifts from that helper, the alignment is a non-conformance.

6. Three-state input completeness flag (concern #8)

The §2 G10 7-row table evaluates first-match across (ai_used × per-category-state). Field-level computation:

• ai_used ∈ {true, false, unset}.
• Each v3.2 category ∈ {USED, NOT USED, UNCERTAIN, not-supplied}.
• First-match-wins evaluation across §2's 7 rows.
• Row-4 partial-state composition per concern #6 resolution: USED at full strength; per-facet annotation for each still-UNCERTAIN; auto-promotion forbidden.

The §4.3 invariants constrain the evaluation:

• G1 invariant — no ai_disclosure field is read from / written to the corpus entry schema; all input flows through the renderer's runtime input contract.
• G2 invariant — track selection reads slr_lineage first, never derives SLR-status from origin_mode alone.
• G3 / G10 invariant — the 7-row table holds; auto-promotion forbidden.
• G4 invariant — 4 anchors, Nature dedup via shared source.
• G5 invariant — three gates for M6 prompts.
• G7 invariant — anchor-specific carve-out semantics.
• G8 invariant — IEEE paired-mandate (row 5 + row 6).
• G9 invariant — anchor-specific image-rights regimes.

7. §4.4 concern resolutions reference

For audit traceability, this protocol implements each Decision Doc §4.4 open concern as follows. See implementation spec §3 for full rationale.

• concern #1 — Track-selection lookup mechanism resolved as: explicit slr_lineage input from pipeline orchestrator; cold-start mode= parameter.
• concern #2 — Tool identity collection: auto-detect from session metadata (v3.2 Phase 4 pattern); explicit fallback per tool for cold-start or non-Claude pipelines.
• concern #3 — Prompt scope: per-(tool × task) tuple across M3.a 6-stage enum; missing tuples emit "not supplied" annotation per tuple.
• concern #4 — IEEE section locator: free-form list with recommended IMRaD exemplars; parallel to G8 level_of_involvement design.
• concern #5 — Nature image metadata + labelling: hybrid output channel — standalone annotation block + suggested inline manuscript patches; ARS does not modify manuscript source autonomously.
• concern #6 — UNCERTAIN per-facet finalization: USED facets render at full strength; UNCERTAIN facets surface per-facet annotation immediately after each render slot.
• concern #7 — Venue + anchor conflict: reject with explicit error citing the policy conflict; silent precedence forbidden.
• concern #8 — Three-state completeness flag: full spec encoded in §6 above.
• concern #9 — Test set scope: covers §4.3 8 invariants + §4.4 #1–#8 + #10 + #11; positive + negative fixture per resolved path / forbidden path.
• concern #10 — ai_used: true substantive-content gate: bare-flag input treated as prompt-trigger forcing v3.2 categorization flow before any anchor render.
• concern #11 — G1 invariant scope: §2.1 G1 Decision authoritative (no ai_disclosure field added to corpus entry schema); non-renderer code changes for §4.4 #1 pipeline-plumbing permitted (pipeline orchestrator setting slr_lineage is not corpus-schema mutation).

8. Related

• Decision Doc: ../docs/design/2026-05-14-ai-disclosure-schema-decision.md
• Implementation spec: ../docs/design/2026-05-14-ai-disclosure-impl-spec.md
• Anchor data table (consumer of this protocol): policy_anchor_table.md
• v3.2 disclosure mode protocol (parallel track): disclosure_mode_protocol.md
• v3.2 venue disclosure policies (Nature dedup peer): venue_disclosure_policies.md
• Shared Nature policy source (canonical pointer, forthcoming): shared/policy_data/nature_policy.md
• Lint contract: ../../scripts/check_policy_anchor_protocol.py
• Conformance test suite: ../../scripts/test_policy_anchor_disclosure.py (Task #7)