medsci-skills 4.1.0

package/skills/grant-builder/SKILL.md

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+---
+name: grant-builder
+description: >
+  Grant and challenge proposal support for radiology and medical AI projects. Structures significance,
+  innovation, approach, milestones, and consortium roles while keeping claims evidence-based and executable.
+triggers: grant, proposal, aims page, grant proposal, significance, innovation, approach, milestones, 산학과제, 산학협력, 과제계획서, 연구계획서, 연구비 신청, 첨부3
+tools: Read, Write, Edit, Bash, Grep, Glob
+model: inherit
+---
+
+# Grant-Builder Skill
+
+## Purpose
+
+This skill supports competitive proposal writing for:
+
+- national R&D grants
+- multi-institution consortia
+- challenge proposals
+- internal pilot funding
+- translational medical AI project plans
+- **Korean government grants** (산학협력 / 연구계획서 — MOHW 복지부, MOTIE 산자부, MSS 중기부, and regional industry-academia programs)
+
+It is optimized for projects where clinical relevance, multi-site coordination, and executable milestones matter as much as technical novelty.
+
+---
+
+## Korean Government Grant Mode (산학과제 / 연구계획서)
+
+When the user requests a Korean industry-academia grant (산학과제) or research plan
+(연구계획서), apply the adaptations below. Korean program terms are preserved in
+parentheses because they are the literal form used on the funding agency's template.
+
+### Document Structure (three-attachment format)
+
+Most Korean grants follow a standardized three-attachment format:
+- **Attachment 1 (첨부1, 기본정보)**: project title, participating institutions,
+  investigator CVs, publication / patent record.
+- **Attachment 2 (첨부2, 매칭확인서)**: per-institution cost-share confirmation,
+  typically finalized after a kickoff meeting between the institutions.
+- **Attachment 3 (첨부3, 연구계획서)**: the 10-page research plan — structure below.
+
+### Attachment 3 Standard Structure
+
+```
+1. Significance & Aims (약 2p)
+   - clinical problem with quantitative framing
+   - domestic + international trends (3–5 year literature / guideline window)
+   - differentiation of the proposed work
+
+2. Research Content & Methods (약 4p)
+   - staged roadmap (Phase 1 – N with time ranges)
+   - pipeline schematic (mandatory when an AI pipeline is in scope)
+   - per-subproject institution and personnel assignment
+
+3. Team Capability (약 1p)
+   - expertise + representative record (SCI papers, patents) per investigator
+   - cross-institution synergy (hospital = data / clinical; university = algorithm)
+
+4. Expected Outcomes & Utilization (약 2p)
+   - quantitative targets: SCI papers, patents
+   - qualitative targets: clinical impact, standardization contribution
+   - linkage to follow-on larger grants (positioning as a seed)
+
+5. Budget Plan (약 1p)
+   - RA salaries, computing equipment, consumables, academic activities, indirect costs
+```
+
+### Writing Tips for Small-Scale Grants (< KRW 30 million)
+
+- Write for a non-specialist reviewer — assume the evaluator is not in your subfield.
+- Emphasize feasibility over technical novelty.
+- Prioritize length / format compliance; exceeding the template incurs scoring penalties.
+- Include preliminary data or pilot results whenever available.
+- Keep quantitative targets conservative — undershooting a committed target is punished
+  more than overdelivering on a modest one.
+
+---
+
+## Communication Rules
+
+- Communicate with the user in their preferred language.
+- Proposal prose should be in the language required by the target call.
+- Avoid hype. Emphasize unmet need, feasibility, differentiation, and deliverables.
+
+---
+
+## Core Outputs
+
+Depending on the request, produce one or more of:
+
+- project concept summary
+- `Significance`
+- `Innovation`
+- `Approach`
+- specific aims
+- work packages
+- milestone table
+- role split by institution
+- evaluation framework
+- reviewer-risk memo
+
+---
+
+## Workflow
+
+### Phase 1: Decode the funding call
+
+Extract:
+- funding body
+- call theme
+- eligibility constraints
+- deliverable expectations
+- timeline
+- evaluation criteria
+
+If no call text is available, infer a generic academic-medical AI proposal structure and label assumptions.
+
+### Phase 2: Frame the problem
+
+Define:
+- clinical pain point
+- current workflow limitation
+- why existing AI or standard care is insufficient
+- who benefits if the project succeeds
+
+**Gate:** Present the problem framing (clinical pain point, gap, proposed solution) to the
+user. Confirm before building proposal sections — a misframed problem produces an
+unfundable proposal.
+
+### Phase 3: Build the proposal spine
+
+Always articulate:
+- problem
+- gap
+- proposed solution
+- why this team can execute it
+- measurable outputs
+
+### Phase 4: Convert to proposal sections
+
+#### Significance
+
+Must answer:
+- why this matters clinically
+- why this matters now
+- why the proposed solution is worth funding
+
+#### Innovation
+
+Should focus on:
+- what is genuinely different
+- why the integration is new
+- why the novelty is useful, not just technical
+
+#### Approach
+
+Should define:
+- dataset and participating sites
+- model or workflow components
+- validation plan
+- benchmark/comparator
+- failure analysis
+- risk mitigation
+
+### Phase 5: Execution plan
+
+Generate:
+- milestones by quarter or year
+- institution-level responsibilities
+- dependencies and handoffs
+- required infrastructure
+
+---
+
+## Default Structure
+
+```text
+## Proposal Summary
+Title: ...
+Goal: ...
+Clinical problem: ...
+
+### Significance
+...
+
+### Innovation
+...
+
+### Approach
+Aim 1. ...
+Aim 2. ...
+Aim 3. ...
+
+### Milestones
+- ...
+
+### Consortium roles
+- ...
+
+### Major risks and mitigations
+- ...
+```
+
+---
+
+## Evaluation Heuristics
+
+Before finalizing, check:
+
+1. Is the clinical need explicit and credible?
+2. Is the novelty more than "we will use AI"?
+3. Are the aims linked to measurable outputs?
+4. Is the validation plan convincing?
+5. Is the multi-site structure realistic?
+6. Are compute, annotation, and regulatory needs acknowledged?
+7. Does each institution have a distinct role?
+
+---
+
+## Common Weaknesses To Flag
+
+- novelty described without clinical consequence
+- vague benchmark or success criterion
+- no external validation or deployment path
+- too many aims for the timeline
+- consortium members listed but not functionally integrated
+- proposal sounds like a paper, not a funded program
+
+---
+
+## Handoff Rules
+
+- route to `search-lit` to support significance and prior-art positioning
+- route to `design-study` if the evaluation framework is weak
+- route to `write-paper` only when the proposal requires publication-style narrative sections
+
+---
+
+## What This Skill Does NOT Do
+
+- It does not fabricate budget details
+- It does not promise datasets, partners, or infrastructure not evidenced by the user
+- It does not replace institutional administrative review
+
+## Anti-Hallucination
+
+- **Never fabricate references.** All citations must be verified via `/search-lit` with confirmed DOI or PMID. Mark unverified references as `[UNVERIFIED - NEEDS MANUAL CHECK]`.
+- **Never invent clinical definitions, diagnostic criteria, or guideline recommendations.** If uncertain, flag with `[VERIFY]` and ask the user.
+- **Never fabricate numerical results** — compliance percentages, scores, effect sizes, or sample sizes must come from actual data or analysis output.
+- If a reporting guideline item, journal policy, or clinical standard is uncertain, state the uncertainty rather than guessing.

package/skills/grant-builder/skill.yml

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+schema_version: 2
+name: grant-builder
+layer: C
+owner_domain: grant_proposal
+
+when_to_use: "Support grant and challenge proposals (significance, innovation, approach, milestones, consortium roles) with evidence-based, executable claims."
+when_NOT_to_use: "IRB protocol content (use write-protocol); manuscript drafting (use write-paper)."
+
+inputs:
+  - "funding call / RFP"
+  - "project concept"
+  - "team/consortium"
+outputs:
+  - "proposal sections (significance, innovation, approach, milestones)"
+side_effects:
+  - writes_project_artifacts
+downstream_consumers:
+  - write-protocol
+forbidden_actions:
+  - fabricate_preliminary_data_or_citations
+  - promise_unexecutable_milestones
+
+# v2.1 quality card
+purpose: "Structure a fundable, executable proposal whose claims are evidence-based and whose milestones are realistic."
+safety_boundaries:
+  - "Claims are tied to evidence the user supplies; preliminary data and citations are not invented."
+  - "Milestones are scoped to be executable, not aspirational."
+known_limitations:
+  - "Does not guarantee funding; tailoring to a specific reviewer panel is the user's responsibility."
+  - "No standalone demo; content requires PI review."
+validation_commands:
+  - "/verify-refs --strict on any cited work"
+  - "/self-review for internal consistency"
+evidence_surface: manual_workflow

package/skills/humanize/SKILL.md

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+---
+name: humanize
+description: Detect and remove AI writing patterns from academic manuscripts and response-to-reviewers letters. Scans for 24 common AI-generated text patterns and rewrites flagged passages to sound naturally human-written while preserving technical accuracy.
+triggers: humanize, AI patterns, AI 문체, remove AI writing, make it sound natural, 자연스럽게, de-AI
+tools: Read, Write, Edit, Grep, Glob
+model: inherit
+---
+
+# Humanize Skill
+
+You are assisting a medical researcher in detecting and removing AI writing patterns from
+academic manuscripts. Your goal: make the text read as if an experienced academic physician
+wrote it, while preserving every technical claim, number, and citation.
+
+## Communication Rules
+
+- Communicate with the user in Korean (matching their working language).
+- All manuscript edits are in English.
+- Medical terminology is always in English, even in Korean communication.
+
+## Reference Files
+
+- **Pattern reference**: `${CLAUDE_SKILL_DIR}/references/ai_patterns.md` -- full 24-pattern list with expanded examples for medical/radiology manuscripts (Pattern 19–21 are senior-MA-reviewer red flags; Pattern 22–24 are response-to-reviewers letter patterns)
+- **Source material**: Based on matsuikentaro1/humanizer_academic and Wikipedia: Signs of AI writing
+
+Always read the pattern reference file at the start of a humanize session.
+
+---
+
+## Workflow
+
+### Phase 1: Scan
+
+Read the manuscript section(s) provided by the user and scan for all 24 patterns. For
+response-to-reviewers letters and cover letters, prioritise patterns 22-24.
+
+**For each pattern found:**
+1. Record the pattern number and name.
+2. Count occurrences.
+3. Extract the exact passage from the text.
+4. Note the location (paragraph number or line range).
+
+**Output: Pattern Frequency Table**
+
+```
+## AI Pattern Scan Report
+
+Section: {section name}
+Word count: {N}
+
+| # | Pattern | Count | Severity | Example from text |
+|---|---------|-------|----------|-------------------|
+| 1 | Significance inflation | 3 | HIGH | "...pivotal role in diagnostic imaging..." |
+| 7 | AI vocabulary words | 5 | HIGH | "Additionally,...", "crucial finding..." |
+| 8 | Copula avoidance | 2 | MEDIUM | "...serves as the gold standard..." |
+| ... | ... | ... | ... | ... |
+
+Patterns not detected: 2, 4, 9, 14, 15
+
+Total AI pattern instances: {N}
+AI pattern density: {N per 1000 words}
+```
+
+### Phase 2: Report
+
+Present findings to the user with actionable summary.
+
+**Severity levels:**
+- **HIGH** (>3 occurrences): Likely to trigger AI detection tools. Fix immediately.
+- **MEDIUM** (1-3 occurrences): Noticeable to careful readers. Should fix.
+- **LOW** (0 occurrences): Clean for this pattern.
+
+**AI Pattern Score:**
+- Count total pattern instances across all 24 categories.
+- Compute density: instances per 1000 words.
+- Target: < 2.0 instances per 1000 words.
+
+**Gate:** Present the report and ask the user which patterns to fix. Default: fix all HIGH and MEDIUM.
+
+### Phase 3: Fix
+
+Rewrite flagged passages following these rules:
+
+1. **Preserve technical accuracy.** Every number, statistic, p-value, confidence interval, and
+   clinical fact must remain identical.
+2. **Preserve citation density.** Do not remove or relocate citations.
+3. **Preserve formal academic register.** Do not make the text casual or conversational.
+4. **Do not force casualness.** The target voice is an experienced radiologist writing for peers
+   in a top-tier journal -- not a blog post.
+5. **Keep domain-specific terminology intact.** "Convolutional neural network," "apparent diffusion
+   coefficient," "Fleiss' kappa" stay as-is.
+6. **Never introduce new claims** or remove existing ones.
+7. **Vary sentence structure.** Mix short declarative sentences (8-12 words) with longer ones
+   (25-35 words). Avoid uniform length.
+8. **Use active voice** where natural. "We analyzed" rather than "Analysis was performed."
+
+**Fix strategies per pattern category:**
+
+| Category | Strategy |
+|----------|----------|
+| Content patterns (1-6) | Delete vague claims; replace with specific data or citations |
+| Language patterns (7-12) | Substitute with plain academic English; simplify verb constructions |
+| Style patterns (13-15) | Adjust formatting and punctuation |
+| Filler and hedging (16-18) | Delete filler; calibrate hedging to match evidence level |
+
+**Output:** Present the rewritten text with changes highlighted using diff format or tracked changes.
+
+### Phase 4: Verify
+
+Re-scan the rewritten text using the same 24 patterns.
+
+**Output: Verification Report**
+
+```
+## Verification Report
+
+| Metric | Before | After |
+|--------|--------|-------|
+| Total instances | 23 | 4 |
+| Density (per 1000 words) | 8.2 | 1.4 |
+| HIGH severity patterns | 3 | 0 |
+| MEDIUM severity patterns | 5 | 2 |
+
+Remaining issues:
+- Pattern 17 (hedging): 2 instances remain -- appropriate for the evidence level.
+
+Verdict: PASS (density < 2.0)
+```
+
+If the density remains above 2.0, run another fix-verify cycle (max 3 rounds).
+
+---
+
+## The 24 Detection Patterns
+
+### Content Patterns
+
+| # | Pattern | What to look for | Fix |
+|---|---------|------------------|-----|
+| 1 | Significance inflation | "pivotal," "evolving landscape," "underscores the critical importance" | Delete or state the specific importance with data |
+| 2 | Notability claims | "landmark trial," "renowned investigators," "groundbreaking" | Remove; let the data speak |
+| 3 | Superficial -ing analyses | "highlighting the cardioprotective effects," "underscoring the broad applicability" | End the sentence at the data; start a new sentence for interpretation |
+| 4 | Promotional language | "remarkable findings," "dramatic reductions," "profound impact" | State the actual numbers neutrally |
+| 5 | Vague attributions | "Studies have shown," "Experts argue," "Several publications" | Cite the specific study |
+| 6 | Formulaic challenges sections | "Despite challenges... future outlook... continues to provide" | State specific limitations factually |
+
+### Language Patterns
+
+| # | Pattern | What to look for | Fix |
+|---|---------|------------------|-----|
+| 7 | AI vocabulary words | Additionally, crucial, delve, enhance, fostering, pivotal, showcase, tapestry, underscore, landscape (abstract) | Delete or replace with plain English |
+| 8 | Copula avoidance | "serves as," "stands as," "represents a" | Use "is" |
+| 9 | Negative parallelisms | "not only X but also Y" | "X and Y" |
+| 10 | Rule of three overuse | Forcing ideas into groups of three repeatedly | Use natural grouping (2, 4, 5 items) |
+| 11 | Synonym cycling | patients/participants/subjects/individuals | Pick one term, use consistently |
+| 12 | False ranges | "from improved renal function to enhanced cardiac outcomes" | List the specific outcomes directly |
+
+### Style Patterns
+
+| # | Pattern | What to look for | Fix |
+|---|---------|------------------|-----|
+| 13 | Em dash overuse | More than 2 em dashes per page | Use parentheses or restructure |
+| 14 | Title case in headings | "Statistical Analysis And Primary Endpoints" | Sentence case per journal style |
+| 15 | Curly quotation marks | Curly quotes from ChatGPT | Straight quotes |
+
+### Filler and Hedging
+
+| # | Pattern | What to look for | Fix |
+|---|---------|------------------|-----|
+| 16 | Filler phrases | "It is important to note that," "In order to," "Due to the fact that" | Delete the filler; state the content directly |
+| 17 | Excessive hedging | "may potentially suggest the possibility" | Choose the appropriate certainty level: "suggests" |
+| 18 | Generic positive conclusions | "The future looks bright," "continues to reshape," "paves the way" | State the specific next step or implication |
+
+### Senior MA Reviewer Patterns
+
+| # | Pattern | What to look for | Fix |
+|---|---------|------------------|-----|
+| 19 | § (section sign) marker | "as in §2.3", "(see §Discussion)", "§Results" | Delete or replace with section name ("Methods", "Results") — `grep -c "§"` = 0 |
+| 20 | Methods/Results self-reference parenthetical | "(Methods §X)", "(Results §3.1)", "(Methods, Section 2.3)" | Drop the parenthetical or shorten to "(see Methods)" |
+| 21 | AI Disclosure boilerplate (body) | "## Artificial Intelligence Disclosure", "Generative AI was not used to create..." in manuscript body | Remove from body → place in cover letter / submission form only (per `~/.claude/rules/journal-ai-image-policies.md`) |
+
+### Response-Letter Patterns (R2R)
+
+Patterns 22-24 apply only when scanning a response-to-reviewers letter or editor cover letter,
+not manuscript bodies. To avoid drift, they are defined once — with triage detection, the
+editing-mechanism-vs-analysis distinction, and before/after examples — in
+`${CLAUDE_SKILL_DIR}/references/ai_patterns.md` (Response-Letter Patterns section). For authoring
+guidance and the full gallery, see the revise skill's `references/r2r_voice.md`.
+
+---
+
+## Section-Specific Focus
+
+When scanning a full manuscript, prioritize these patterns per section:
+
+| Section | Priority Patterns | Reason |
+|---------|------------------|--------|
+| Abstract | ALL (1-21) | Most visible section; most scrutinized for AI patterns |
+| Introduction | 1, 2, 5, 7, 12 | AI inflates background importance and uses vague attributions |
+| Methods | 8, 16 | Methods should be straightforward; copula avoidance and filler are common |
+| Results | 3, 4, 6, 10, 11 | AI adds interpretive -ing clauses and promotional language to results |
+| Discussion | 1, 5, 6, 17, 18 | AI produces formulaic discussions with excessive hedging |
+| Conclusion | 1, 18 | AI generates generic positive conclusions |
+| Methods (MA / SR) | 19, 20, 21 | § markers, self-reference parentheticals, AI Disclosure boilerplate are senior-MA-reviewer red flags |
+| Discussion (MA / SR) | 19, 20 | Self-reference parentheticals especially common when discussing methods |
+| Body (any) | 21 | AI Disclosure belongs in cover letter / submission form, not manuscript body |
+| Response to Reviewers / cover letter | 22, 23, 24 (+ 13, 16, 19) | Editing-mechanism narration, internal draft line numbers, and tooling leaks are the dominant tells in machine-drafted rebuttals (see ai_patterns.md R2R section) |
+
+---
+
+## Interaction with Other Skills
+
+| Calling skill | When this skill is invoked |
+|---------------|---------------------------|
+| `/write-paper` | Phase 7 (Polish) -- automatic scan before submission |
+| `/peer-review` | When reviewing one's own manuscript for AI patterns |
+| `/revise` | When drafting response-to-reviewers letters and cover letters -- patterns 22-24 are the enforced gate before submission |
+
+When called by another skill, return the verification report so the calling skill can check
+the pass/fail status.
+
+---
+
+## What This Skill Does NOT Do
+
+- Does not evaluate scientific quality, accuracy, or completeness of the manuscript.
+- Does not add new content or citations.
+- Does not assess journal compliance or formatting.
+- Does not translate between languages.
+- Only removes AI patterns; does not perform general copy-editing.
+
+## Anti-Hallucination
+
+- **Never introduce new claims or citations** during rewriting. Every technical fact, number, and reference must remain identical to the original.
+- **Never remove existing citations** or relocate them during pattern fixes.
+- **Never change the meaning** of a sentence while fixing AI patterns — only rephrase, never reinterpret.
+- If a passage cannot be fixed without changing its meaning, flag it for the user rather than guessing.
+
+---
+
+## Gates
+
+| Gate | Severity | Trigger | Action on fail |
+|---|---|---|---|
+| AI-pattern density target | ADVISORY | density > 2.0 patterns / 1000 words after sweep | warn; surface remaining flagged passages for manual review |
+| Pattern 19 — `§` symbol | ENFORCED (senior MA reviewer prep) | `grep -c "§" manuscript.md` > 0 | auto-strip; verify post-rewrite count == 0 |
+| Pattern 20 — `(see Methods §X)` self-reference | ENFORCED | match found | rewrite to direct section name reference |
+| Pattern 21 — AI Disclosure paragraph in body | ENFORCED | "Generative AI was not used..." paragraph in manuscript body | move to cover letter or remove |
+| Patterns 22-24 — R2R editing-mechanism / draft line-number / tooling leak | TRIAGE (response letters); `§` = 0 hard | detection greps in ai_patterns.md R2R section surface candidates | review each hit (analysis narration, quoted additions, revised-manuscript page/line are NOT tells); rewrite confirmed tells to substantive prose |
+| Citation preservation invariant | ENFORCED | any pre-existing `[@bibkey]` removed by rewrite | revert that single rewrite; flag for user |
+| Numerical preservation invariant | ENFORCED | any number changed by rewrite | revert; flag for user |