Plot-Logic-Pipeline

Systematically deconstruct scientific papers by following the figure-discussion logical backbone.

When to Use

• - Analyzing a research paper's argument structure
• Reviewing manuscripts before submission
• Understanding how figures support claims in technical papers
• Mapping evidence sources (literature vs. new measurements)
• Identifying logical gaps or unsupported claims

Core Principle

Figures are the bare bones of a paper's logic flow. Each figure corresponds to a discussion that either:

• - Sets up the next key finding (preparation)
• States the key finding (conclusion)

Complete understanding requires analyzing every figure-discussion pair and tracking evidence sources.

Analysis Framework

Step 1: Figure Inventory

Create a complete inventory of all figures in the paper:

CODEBLOCK0

Step 2: Figure-Discussion Mapping

For each figure, identify its corresponding discussion section and analyze:

CODEBLOCK1

Step 3: Logic Flow Reconstruction

Map how figures build upon each other:

CODEBLOCK2

Step 4: Evidence Assessment

Evaluate the strength of the paper's argument:

• - Are all major claims supported by figures?
• Are evidence sources properly attributed?
• Are there logical gaps between figures?
• Do setup discussions adequately prepare for key findings?

Evidence Classification

Previous Study Support

• - Direct citation: Specific reference supporting the claim
• Literature consensus: Multiple citations building consensus
• Comparative reference: Contrasting with previous work

This Paper's Contributions

• - New experimental data: Novel measurements with method specified
• Novel calculations: Computational work or modeling
• Reanalysis: New interpretation of existing data

Combined Evidence

• - Validation: New data confirms previous studies
• Extension: New data builds upon previous work
• Contradiction: New data challenges previous findings

Analysis Templates

See TEMPLATES.md for detailed templates including:

• - Basic figure-discussion analysis
• Complete paper analysis workflow
• Materials science specific templates
• Quality assurance checklist

Quality Checks

Before concluding analysis:

• - ✅ All figures mapped to discussions
• ✅ Evidence sources identified for major claims
• ✅ Logic flow clearly traced from introduction to conclusion
• ✅ Setup vs. statement discussions distinguished
• ✅ Contradictions or gaps noted and flagged

Common Pitfalls

• - Skipping "obvious" figures: Even simple schematics contribute to logic flow
• Missing evidence attribution: Always identify if claims come from citations or new work
• Ignoring setup discussions: These are crucial for understanding logical progression
• Overlooking figure details: Axis labels, error bars, and annotations often contain key information
• Conflating correlation with causation: Note when figures show correlation vs. when claims assert causation

Rules

1. 1. Every figure gets analyzed — no skipping, even if it seems straightforward
2. Always classify evidence — distinguish previous work from new contributions
3. Trace the logic chain — show how each figure builds on the previous one
4. Flag gaps honestly — note missing evidence or weak logical connections
5. Separate observation from interpretation — what the figure shows vs. what the authors claim