Paper Analysis

Do NOT use this skill for general theory or definitions — use literature_research instead. Do NOT use this skill for review article content — use review_analysis instead.

Key Principle: Internal References, Not External Citations

The author's papers are included as-is in the thesis LaTeX. Therefore:

• Do NOT rewrite or summarize what the paper already says
• DO extract specific facts, numbers, and methods to reference from contextual chapters
• DO use internal references: "See Chapter 6, Sec. 6.2" or "as detailed in the following paper"
• DO identify the key contributions to highlight in the introductory paragraphs before each paper

Author Papers Mapping

Prerequisites

1. Run source_registry first to obtain 001) source IDs.

MCP Tool Usage

Querying Author Papers

mcp_notebooklm_notebook_query(
    notebook_id="1b7df790-7858-4fc8-879c-39f41238c4ae",
    query="<your question>",
    source_ids=<author_001_ids>,  # from source_registry, only 001) sources
    conversation_id=<previous_id>  # for follow-up drilling
)

Targeting a Specific Paper

When you need details from a single paper, pass only that paper's source ID:

mcp_notebooklm_notebook_query(
    notebook_id="1b7df790-7858-4fc8-879c-39f41238c4ae",
    query="Detail the domain adaptation methodology used in this paper.",
    source_ids=["<paper_4_source_id>"]
)

Query Strategy

1. Methodology Extraction: Ask for step-by-step methods.

   • Prompt: "Based on '001) paper 4', detail the domain adaptation methodology used to handle dataset shift. List the specific steps and techniques."

2. Results Extraction: Ask for specific numbers and figures.

   • Prompt: "Retrieve the forecasted sensitivity to Dark Matter from '001) paper 5'. What are the exact numerical limits?"

3. Choice Justification: Ask why specific decisions were made.

   • Prompt: "Summarize the motivation for targeting unassociated sources as described in the author's papers."

4. Key Contributions: Extract the main takeaway for chapter introductions.

   • Prompt: "What is the single most important contribution of '001) paper 1'? Summarize in 2-3 sentences suitable for an introductory paragraph."

5. Comparison with Literature: Compare author results against the field.

   • Prompt: "How do the results in '001) paper 3' compare to previous constraints on the MSP luminosity function?"

Output

Internal Reference Notes

Structure output as notes for writing contextual chapters:

## Paper [N] — Key Extractions

### Methodology Summary
- [Step 1]: [brief description] → detailed in Sec X.X of the paper
- [Step 2]: [brief description]

### Key Results
- [Result 1]: [exact value/limit]
- [Result 2]: [comparison with prior work]

### Contribution Statement (for chapter intro)
"[2-3 sentence summary of what this paper achieves and why it matters]"

### Transition Points
- **From context chapter to paper**: [how the introductory chapter leads into this paper]
- **From paper to next chapter**: [how this paper's conclusions set up the next chapter]

Knowledge Saving

REQUIRED: Use the knowledge skill (save mode) to persist methodology insights to .agent/knowledge/. The knowledge skill defines the standard file format and handles deduplication.

Usage Examples

Scenario: Describing Methodology

• User: "Explain how we handled the dataset shift in Paper 4."
• Action: Query 001) paper 4 specifically.
• Query: "Based on '001) paper 4', detail the domain adaptation methodology used to handle dataset shift."

Scenario: Reporting Results

• User: "What was the final sensitivity we achieved for the CTA analysis?"
• Action: Query 001) paper 5.
• Query: "Retrieve the forecasted sensitivity to Dark Matter from '001) paper 5'."

Scenario: Building a Chapter Introduction

• User: "Write the introduction for Chapter 6, before Paper 1 is inserted."
• Action: Query 001) paper 1 for key contributions.
• Query: "What is the key contribution and motivation of '001) paper 1'? What existing gap does it fill?"