Zaoqu-Liu/manuscript-review-revise

Manuscript Review & Revision System

Evaluate and improve scientific manuscripts through a closed-loop process: Score → Identify Weaknesses → Revise → Re-score → Compare. Inspired by APRES (Meta Superintelligence Labs, ICLR 2026).

Core Principles

1. Never modify core scientific claims — preserve all data, results, and conclusions
2. Never add unverified data or fabricated citations — only restructure existing content
3. Every revision has a stated reason — traceable, auditable changes
4. Quantitative before/after comparison — ScholarEval scores pre and post revision
5. Improve presentation, not science — clarity, structure, flow, completeness

When to Use

• User says /review or /review <path-to-manuscript>
• User asks "帮我审一下这篇论文" or "review my manuscript"
• User asks "润色" or "polish this draft"
• After ScienceClaw generates a research report, offer: "需要用审修系统优化这份报告吗？"

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Workflow

Phase 1: ScholarEval Assessment (8 Dimensions)

Score the manuscript on each dimension (0.00–1.00):

| Dimension | Weight | Evaluation Criteria | |-----------|--------|-------------------| | Novelty | 15% | Does this advance knowledge? Are claims clearly differentiated from prior work? | | Rigor | 25% | Methodology sound? Statistics correct? Controls adequate? Sample sizes reported? | | Clarity | 10% | Writing clear? Figures self-explanatory? Logical flow between sections? | | Reproducibility | 15% | Methods detailed enough to replicate? Software versions stated? Data accessible? | | Impact | 20% | Does this matter for the field? Broad or narrow implications? | | Coherence | 10% | Do all parts fit together? Introduction → Methods → Results → Discussion aligned? | | Limitations | 3% | Are limitations honestly acknowledged? Not buried or trivialized? | | Ethics | 2% | Ethical standards met? IRB mentioned if applicable? Conflicts disclosed? |

Compute weighted average. Output initial verdict: accept (≥0.75), minor_revision (≥0.60), major_revision (≥0.40), reject (<0.40).

Phase 2: Citation-Impact Heuristics

Evaluate 10 presentation factors that predict higher citation impact:

| # | Factor | Check | Weight | |---|--------|-------|--------| | 1 | Title specificity | Contains key finding or quantitative result? Not vague? | High | | 2 | Abstract conclusion | Has a clear, quantitative take-home message? | High | | 3 | Figure self-sufficiency | Can each figure be understood from its caption alone? | High | | 4 | Methods reproducibility | Software versions, parameters, thresholds all stated? | Medium | | 5 | Statistical reporting | Effect sizes + CIs alongside p-values? Test assumptions verified? | Medium | | 6 | Discussion balance | Presents counter-arguments and alternative interpretations? | Medium | | 7 | Limitations honesty | Dedicated section with specific (not generic) limitations? | Medium | | 8 | Introduction funnel | Narrows from broad context → gap → specific question? | Low | | 9 | Reference recency | Includes papers from last 2 years? Not relying on outdated reviews? | Low | | 10 | Data availability | States where data/code can be accessed? | Low |

Score each 0–1. Flag factors scoring below 0.5 as revision targets.

Phase 3: Generate Revision Plan

Sort all identified weaknesses by estimated impact on manuscript quality. Output a numbered revision plan:

## 修订计划（按影响力排序）

1. [HIGH] 标题过于笼统 → 改为包含主要发现的具体标题
   当前: "The Role of THBS2 in Cancer"
   建议: "THBS2 Overexpression Associates with M2 Macrophage Infiltration and Poor Survival Across 17 Cancer Types"
   理由: 具体标题平均被引用量高 22%（Paiva et al., 2012）

2. [HIGH] 摘要缺少定量结论 → 添加关键数字
   当前: "THBS2 was significantly upregulated in multiple cancers"
   建议: "THBS2 was significantly upregulated in 17/33 TCGA cancer types (Wilcoxon p<0.001), with highest expression in PAAD (HR=2.31, 95%CI: 1.45-3.68)"
   理由: 摘要中包含具体数字的论文被引用量高 29%

3. [MEDIUM] Figure 2 caption 缺少统计方法说明
   ...

Phase 4: Execute Revisions

Apply each revision to the manuscript text. For each change:

• Quote the original text (2-3 lines of context)
• Show the revised text
• State the reason

Constraints:

• Do NOT change any data values, p-values, effect sizes, or sample sizes
• Do NOT add citations that were not in the original or verified through tools
• Do NOT change the interpretation of results
• Do NOT add new claims or conclusions
• DO improve: titles, headings, topic sentences, transitions, figure captions, methods detail, limitation specificity, discussion balance

Phase 5: Re-score and Compare

Re-run ScholarEval on the revised manuscript. Output comparison:

## 审修效果对比

| Dimension      | Before | After | Change |
|---------------|--------|-------|--------|
| Novelty       | 0.72   | 0.72  | —      |
| Rigor         | 0.68   | 0.75  | +0.07  |
| Clarity       | 0.55   | 0.78  | +0.23  |
| Reproducibility| 0.60  | 0.82  | +0.22  |
| Impact        | 0.70   | 0.70  | —      |
| Coherence     | 0.65   | 0.80  | +0.15  |
| Limitations   | 0.40   | 0.75  | +0.35  |
| Ethics        | 0.90   | 0.90  | —      |
|               |        |       |        |
| **Weighted**  | **0.66**| **0.76** | **+0.10** |
| **Verdict**   | minor_revision | accept | ⬆ |

Citation-impact heuristics: 4/10 → 8/10 factors above threshold

共执行 12 处修订，主要改善了清晰度（+0.23）和可复现性（+0.22）。
核心科学主张和数据未做任何修改。

Phase 6: Output

Save revised manuscript and revision report:

outputs:
  📄 reports/manuscript_revised.md      — 修订后的完整稿件
  📋 reports/revision_report.md         — 修订报告（所有变更 + 理由）
  📊 reports/scholareval_comparison.md  — 评分对比表

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Revision Patterns Library

Title Improvements

| Pattern | Before | After | |---------|--------|-------| | Add key finding | "Role of X in Y" | "X Promotes Y Through Z Mechanism" | | Add quantitative | "X is associated with Y" | "X Overexpression in N/M Cancers Associates with Poor Survival (HR=...)" | | Add scope | "Study of X" | "Pan-Cancer Analysis Reveals X as..." |

Abstract Improvements

• Add sample sizes: "patients" → "patients (n=438)"
• Add effect sizes: "significantly different" → "significantly different (Cohen's d=0.82)"
• Add confidence intervals: "HR=2.31" → "HR=2.31 (95%CI: 1.45–3.68)"

Methods Improvements

• Add software versions: "R" → "R 4.3.2"
• Add package versions: "survival package" → "survival package (v3.5-7)"
• Add thresholds: "significant genes" → "genes with |log2FC|>1 and FDR<0.05"
• Add normalization: "normalized data" → "TMM-normalized counts (edgeR v3.40.2)"

Discussion Improvements

• Add counter-argument paragraph: "However, alternative explanations include..."
• Add comparison with conflicting studies: "In contrast to [Author, Year] who found..."
• Convert generic limitations to specific: "small sample size" → "limited sample size in the PAAD cohort (n=178) may reduce power to detect survival differences in subgroup analyses"

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Integration with Other Skills

• After any Research Recipe completion, offer: "需要用审修系统优化报告吗？输入 /review"
• Works on any markdown file in the project directory
• Can be applied to user-uploaded manuscripts (paste text or provide file path)