| name | paper-extract |
| description | Use when extracting and analyzing academic papers from PDF or LaTeX sources. Use when the user provides a paper, asks to analyze a paper, understand a paper's contributions, decompose a paper into HLS components, or needs a structured paper breakdown with Overview, Big Background, Small Background, Problems, Root Cause, Key Idea, Design Points, and System evaluation. |
Paper Extract — Reverse HLS Decomposition
Overview
Inverse of paper-writing HLS: decomposes a paper into HLS components for deep understanding, gap identification, and research positioning. Outputs in OKF format (YAML frontmatter + structured Markdown) for knowledge graph integration.
Templates → templates/. OKF format → references/okf-format.md.
When to Use
Decision flowchart → references/decision-flow.md.
Use when: user provides PDF/LaTeX to analyze; literature review; pre-review deep read; gap identification; paper comparison.
Don't use for: writing → paper-writing; reviewer feedback → paper-review; figures → paper-plot.
Process Flow
| Phase | Role | Output | Template |
|---|
| E0 | Extractor — text + figures from PDF/LaTeX | output/analysis/ | — |
| E1 | Decomposer — HLS 7+1 core points with evidence | l0.md (OKF) | templates/l0.md |
| E1.5 | Condenser — TLDR, Abstract+Intro only | tldr.md (OKF) | templates/tldr.md |
| E2 | Architect — Section flow chains | l1.md (OKF) | templates/l1.md |
| E3 | Critic — innovation, gaps, positioning | output/analysis/critical-assessment.md | — |
All E1/E1.5/E2 outputs include OKF YAML frontmatter (type, title, description, tags, status, level, generated, sources).
Output layout → references/extraction-guide.md.
Hard Gates
Full text + figure PNGs + captions + references extracted. Verify `output/analysis/full-text.md` and `figures/` exist.
l0.md` with OKF frontmatter and evidence citations. Descriptive, not evaluative. Overview ≤5 sentences. Key Idea = 1 sentence.
Template → [templates/l0.md](templates/l0.md).
<HARD-GATE-E1.5>
TLDR from Abstract+Intro ONLY. OKF frontmatter REQUIRED. Structured (1)(2)(3) sub-points, 1-2 sentences each. No [MISSING].
Template → templates/tldr.md.
</HARD-GATE-E1.5>
Each Section's A→B→C chain + figure placements + mermaid dependency graph. OKF frontmatter REQUIRED.
Template → [templates/l1.md](templates/l1.md)
Each Section's A→B→C chain + figure placements + dependency graph. User confirms.
Innovation level + 3 strengths + 3 weaknesses + gap analysis + positioning map. Every claim cites paper text.
E1: The 7+1 Core Points
| # | Point | Question Answered | Paper Section Clue |
|---|
| 1 | Overview | What does this paper do in one paragraph? | Abstract + Introduction |
| 2 | Big Background | What broad research wave/trend enables this? | Introduction ¶1-2 |
| 3 | Small Background | What specific prior work does this directly extend? | Introduction ¶3-4, Related Work |
| 4 | Problems | What concrete problems does this paper solve? | Introduction (gap statements), Problem Formulation |
| 5 | Root Cause | What fundamental bottleneck underlies all problems? | Motivation, Design Rationale |
| 6 | Key Idea | What is the ONE core insight? (≤1 sentence) | Introduction (thesis statement), Contribution list |
| 7 | Design Points | What are the 2-5 technical contributions? | Method/Design/Architecture sections |
| +1 | System & Experiment | How was it implemented and evaluated? | Implementation, Evaluation |
For each point: state claim → cite evidence (quote or section:paragraph) → flag [MISSING] if no evidence found.
E1.5: TLDR
Structured (1)(2)(3) sub-points per section, 1-2 sentences each. Abstract+Intro ONLY. Template → references/tldr-format.md.
E2: Section Flow Chains
For each Section: name, purpose, A→B→C chain, figure refs to output/analysis/figures/, dependencies. Dependency graph → references/extraction-guide.md.
E3: Critical Assessment
Innovation level (Breakthrough/Novel/Incremental/Engineering), 3+ strengths/weaknesses, gap analysis, positioning map (approach type × scope, 3-5 prior works). Details → references/extraction-guide.md.
Quick Reference
| User says | Trigger mode |
|---|
| "Analyze this paper" | E0→E1→E1.5→E2→E3 |
| "Give me a quick summary" | E0→E1→E1.5 |
| "Just the TLDR" | E0→E1.5 |
| "What's the core idea?" | E0→E1 (Key Idea + Design Points) |
| "Find the gaps" | E0→E1→E3 (Gap Analysis) |
| "Compare these two papers" | Full pipeline on both, side-by-side |
| "Is this paper good?" | E0→E1→E3 (Strengths/Weaknesses) |
Source Type Handling
PDF: scripts/extract-pdf.py <paper.pdf> --output output
LaTeX: scripts/extract-latex.py <main.tex> --output output
Details → references/extraction-guide.md. Run scripts with --help for options.
Common Mistakes
| Mistake | Fix |
|---|
| Summarizing instead of decomposing | Each HLS point is a distinct dimension |
| Evaluating during E1 | E1 = descriptive only. Judgment → E3 |
| Fabricating missing points | Mark [MISSING] — don't invent |
| Confusing Problems with Root Cause | Problems = what's broken; Root Cause = WHY |
| Skipping evidence citations | Every hls-L0.md point MUST cite paper text |
| Relying on captions alone | Extract figure images to figures/ for visual inspection |
| TLDR using full paper | TLDR = Abstract+Intro ONLY |
| TLDR as single blob paragraph | Must use (1)(2)(3) line breaks — never a wall of text |
Cross-Skill Integration
| Skill | Relationship |
|---|
| paper-writing | Inverse: paper→HLS vs HLS→paper |
| paper-review | E3 feeds into review dimensions |
| analyze-plot | E2 figure maps guide regeneration |
REQUIRED BACKGROUND: paper-writing's HLS framework (L0 core points, L1 flow chains).
