analyze-paper

name	analyze-paper
description	Extract structured information from a research paper: system model, theorem statements, proof techniques, complexity claims, and red flags. Use when asked to analyze, summarize, or review an academic paper.
user-invocable	true
argument-hint	<paper-path> [--output <path>] [--goal "<goal>"]
license	Apache-2.0
compatibility	Requires PDF reading capability for the paper under analysis.

Analyze Paper

Extract structured information from an academic paper, producing a comprehensive summary that downstream skills can build on.

Usage

Invoke this skill by name with the paper path (and optional flags). On slash-command hosts, prefix with / (e.g. /analyze-paper <args>).

# Analyze the primary paper under study
analyze-paper path/to/paper.pdf

# Analyze a literature paper with research goal as context
analyze-paper reaper-workspace/papers/2024-1234.pdf --goal "post-quantum threshold signatures" --output reaper-workspace/papers/2024-1234-notes.md

Argument parsing: The first non-flag argument is the paper path. Optional flags:

• --output <path>: Write output to the given path instead of the default reaper-workspace/notes/paper-summary.md.
• --goal "<text>": The research goal as additional context. When provided, the output includes a Relevance section assessing how the paper relates to this goal, and reading depth is calibrated by relevance (see Step 1).

Instructions

1. Read the Paper

Read the paper at the provided path using your host's file-read primitive (works for PDFs and text files on hosts that support PDF reading; otherwise extract text first).

Follow the three-pass strategy from ../reaper/references/paper-analysis.md:

• Pass 1 (skeleton): Abstract, introduction, conclusion, theorem statements. Identify the main claims.
• Pass 2 (construction): Protocol details, proof sketches, figures. Understand the key technical idea.
• Pass 3 (proofs): Full formal proofs, appendices, security reductions. Verify logical steps.

When --goal is provided, calibrate depth by relevance to the goal: Pass 1 for all papers; Pass 2 for medium-relevance; all three passes for high-relevance papers.

2. Extract Information

For each section below, extract the relevant information. When extracting theorem statements or formal claims, copy them verbatim — do not paraphrase.

Critical: Distinguish what the paper claims (in the introduction, abstract) from what it actually proves (in the theorems, proofs). Note any discrepancies.

3. Write Output

Write the extracted information to reaper-workspace/notes/paper-summary.md (or the path specified by --output) with the following structure:

# Paper Summary: [Paper Title]

## Metadata
- **Title**:
- **Authors**:
- **Venue/Year**:
- **Paper ID**: (ePrint, arXiv, DOI)
- **Link**: (e.g., https://arxiv.org/abs/XXXX.XXXXX or https://eprint.iacr.org/YYYY/NNNN)

## Problem Statement
What problem does this paper solve? Why does it matter?

## System Model
[Extract all model dimensions relevant to the paper's domain. Consult `../reaper/references/model.md` for the domain-appropriate dimensions to extract. Every applicable dimension must have a concrete answer.]

## Construction Overview
High-level protocol description. Key technical idea. Building blocks used.

## Key Results
List each theorem/claim verbatim:
1. **Theorem X.X**: [exact statement]
   - Model: [exact model under which this is proved]
   - Proof technique: [game-based / simulation / reduction]

## Proof Technique
Overall proof approach. Key lemmas. Reduction chain. Where the corruption threshold and network model are used.

## Complexity Claims
- Communication: 
- Rounds:
- Computation:

## Strengths
[Label each major/minor: novelty, methodology fit, proof rigor, evaluation quality, clarity.]

## Weaknesses
[Label each major/minor/fatal: broken methodology, missing proofs, unjustified claims, unfair comparisons, unclear writing, overclaimed results.]

## Key Definitions and Notation
Non-standard notation. Formal definitions referenced by the proofs.

## Red Flags
Any concerns identified during reading (see `../reaper/references/paper-analysis.md` for common red flags).

## Relevance
[Present ONLY when --goal is provided. Tag one or more: *problem definition*, *formalization*, *solution technique*, *negative result*, *literature/context*, *writing model*. One sentence per tag explaining how this paper relates to the research goal.]

Sections should be proportional to what the paper warrants. If a paper has no complexity claims, omit that section. If the proof technique is trivial, keep it brief. The template is a guide, not a form to fill in mechanically.

Quality Criteria

• Every theorem statement is copied verbatim, not paraphrased
• When a System Model section is present, it covers every dimension that applies to the paper (network, adversary, trust, communication, crypto). Omit the section only if the paper does not warrant it (e.g. pure information-theoretic results); never partially fill it
• Strengths and weaknesses are labeled with severity (major/minor/fatal) and are honest — if the paper looks solid, say so; if there are concerns, list them specifically
• Red flags section is honest — no concerns is a valid answer
• The summary is useful standalone — a reader who hasn't seen the paper should understand the key claims and approach
• When --goal is provided, relevance tags are specific to the goal, not generic ("related to our topic")
• If the PDF is unreadable, try page-by-page with the pages parameter. If it still fails, report the error — do not fabricate a summary