Module: Logical connection and methodological depth

Trigger words: logic, coherence, logic, connection, methodology, methodology, argument, argument

Script Usage:

uv run python $SKILL_DIR/scripts/analyze_logic.py main.typ
uv run python $SKILL_DIR/scripts/analyze_logic.py main.typ --section method

--sectionAccepts canonical keys and synonyms (methods/methodology/approach → method）。

Goal: Ensure logical flow between paragraphs and strengthen methodological rigor.

Key inspection areas:

1. Paragraph-level logical connection (AXES model):

components	illustrate	Example
Assertion (assertion)	A clear topic sentence that states the core idea	"The attention mechanism can improve the effect of sequence modeling."
Xample (example)	Specific evidence or data to support the claim	"In experiments, the attention mechanism achieved 95% accuracy."
Explanation (explanation)	Analyze why the evidence supports the claim	"This improvement comes from its ability to capture long-range dependencies."
Significance (meaning)	Connection to wider argument or next paragraph	"This discovery provides a basis for the architectural design of this article."

2. Transition signal words:

Relationship type	Chinese signal words	English correspondence
progressively	In addition, further and more importantly	furthermore, moreover
turning point	However, but, on the contrary	however, nevertheless
cause and effect	Therefore, it can be seen that therefore	therefore, consequently
order	first, subsequently, finally	first, subsequently, finally
Example	For example, specifically, especially	for instance, specifically

3. Methodological in-depth checklist:

• [ ] Each claim is supported by evidence (data, quotes, or logical reasoning)
• [ ] There are good reasons for the method chosen (why this method rather than another?)
• [ ] Explicit acknowledgment of research limitations
• [ ] Clearly state assumptions
• [ ] Reproducibility details are sufficient (parameters, data sets, evaluation metrics)

4. Frequently Asked Questions:

Question type	Performance	Correction method
logical gap	Lack of cohesion between paragraphs	Add transitional sentences to illustrate paragraph relationships
Unfounded claim	Assertion lacks supporting evidence	Supplementary quotes, data or reasoning
Shallow methodology	"This article adopts X" but there is no reason	Explain why X is suitable for this problem
implicit assumptions	Prerequisites not stated	Explicitly state assumptions

Output format:

// 逻辑衔接（第45行）[Severity: Major] [Priority: P1]: 段落间逻辑断层
// 问题：从问题描述直接跳转到解决方案，缺乏过渡
// 原文：数据存在噪声。本文提出一种滤波方法。
// 修改后：数据存在噪声，这对后续分析造成干扰。因此，本文提出一种滤波方法以解决该问题。
// 理由：添加因果过渡，连接问题与解决方案

// 方法论深度（第78行）[Severity: Major] [Priority: P1]: 方法选择缺乏论证
// 问题：方法选择未说明理由
// 原文：本文采用ResNet作为骨干网络。
// 修改后：本文采用ResNet作为骨干网络，其残差连接结构能有效缓解梯度消失问题，且在特征提取任务中表现优异。
// 理由：用技术原理论证架构选择

Chapter Guide:

chapter	Key points of logical connection	Methodological depth focus
Abstract	The smooth connection of purpose→method→result→conclusion	Highlight core contributions
Introduction	Smooth transition from question → blank → contribution	Demonstrate research significance
Related Work	Group by topic, explicit comparison	The relationship between positioning and previous work
Methods	Logical progression between steps	Justify every design choice
Experiments	Settings→Results→Analysis Process	Explain evaluation metric selection
Discussion	The connection of discovery → enlightenment → limitation	Recognize research boundaries

Best Practice:

1. One paragraph, one topic: Each paragraph focuses on a single core idea
2. Topic sentence first: The first paragraph states the proposition of this paragraph
3. Complete evidence chain: Each claim needs support (data, references or logic)
4. Explicit Transition: Use signal words to indicate paragraph relationships
5. Argument rather than description: explain "why" rather than just state "what"

Reference: WRITING_PHILOSOPHY.md

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Literature Review Quality Validation (A1-A4)

Authoritative rules are defined in latex-paper-en/references/modules/LOGIC.md. This section mirrors them for Typst usage.

A1: Thematic Clustering (Not Author/Year Enumeration)

Related Work must organize references by research theme. Detecting 3+ consecutive sentences following "Author (Year) proposed..." signals enumeration → Major/P1.

Script detection:analyze_logic.pychecks for consecutive author/year enumeration patterns in therelatedsection.

A2: Critical Analysis After Each Theme Cluster (LLM-judgment)

Each thematic group must end with a synthesis sentence that compares or evaluates. Requires LLM judgment.

A3: Research Gap Derivation

The final paragraph of Related Work must contain explicit research gap language. The script scans the last 10 lines for gap keywords (gap|limitation|remains|lack|overlooked|under-explored). No match → Major/P1.

A4: Funnel-Shaped Citation Density (LLM-judgment)

Citation density should follow broad→focused→specific. Requires LLM judgment.

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Cross-Section Logic Chain Closure (C3)

Introduction contribution claims must be answered in the Conclusion. The script extracts contribution keywords fromintroductionand answer keywords fromconclusion. If intro has claims but conclusion has zero answer language → Major/P1 ([Script]observation).

Activate with--cross-sectionflag or full-document analysis (no--section).

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Motivation Red-Thread Closure (opt-in: --motivation-thread)

A strong paper is one problem→solution arc: every Introduction promise should be tested in Results/Experiments and resolved in Discussion/Conclusion. This opt-in diagnostic is additive — without the flag the normal logic output is unchanged.

uv run python scripts/analyze_logic.py main.typ --motivation-thread

Produces (read-only, all[Script], comment prefix//):

• Promise Map — each Introduction promise → best-overlapping Results/Experiment line; [NO EVIDENCE FOUND] = promise never tested.
• Closure Map — each Introduction claim → best-overlapping Discussion/Conclusion line; [UNCLOSED] = claim never resolved.
• Evidence-without-promise — numeric Results lines that trace to no Introduction promise.

Mechanism: keyword + content-token overlap (English words ≥4 chars plus CJK bigrams), so it works on English and Chinese Typst papers alike. It is a heuristic navigation aid, not a verdict — the report says so and asks for manual verification.