AgentSkillsCN

read_paper

将研究论文转化为结构化的Obsidian笔记，并关联相关研究项目。

SKILL.md
--- frontmatter
name: read_paper
description: Convert a research paper into structured Obsidian notes and link research projects

📄 Paper Reading Skill

Read a research paper and convert it into:

  • •one structured paper note
  • •one or more linked research project notes

This skill transforms reading into reusable research ideas.

CRITICAL RULES (NON-NEGOTIABLE)

  • •Paper notes live only in Reading/
  • •Use Templates/Paper Note.md exactly - preserve ALL headings, emojis, and structure
  • •Project notes live only in Projects/
  • •Never create topic notes or concept-only notes
  • •Research ideas always live as project notes
  • •Paper notes must never link to MOCs
  • •Paper notes may link only to:
    • •project notes (in Projects/)
    • •other paper notes (in Reading/)
  • •NO OTHER LINK TYPES ALLOWED - no concepts, no methods, no techniques
  • •Bullet points only — no prose
  • •Aggressive [[wiki linking]] required BUT ONLY to projects/papers

TEMPLATE COMPLIANCE (MANDATORY)

BEFORE starting, read the template:

  1. •Use the view tool to read Templates/Paper Note.md
  2. •Copy the EXACT structure including:
    • •All emoji section headers (🧾, 🌍, ❓, 💡, etc.)
    • •All subsection prompts (### questions)
    • •All markdown formatting
  3. •Fill in content under each subsection prompt
  4. •Do NOT remove, rename, or flatten any sections

Template location: Templates/Paper Note.md

Rules:

  • •Keep ALL emojis exactly as shown in template
  • •Keep ALL section headings exactly as shown in template
  • •Keep ALL subsection prompts (### questions) exactly as shown
  • •Answer each subsection with bullet points below the prompt
  • •Do NOT remove or rename sections
  • •Do NOT flatten the structure
  • •Place project links ONLY in "Linked Research Projects" subsection
  • •Place paper links ONLY in "Connections to Other Work" subsections

LINKING RULES (CRITICAL)

✅ ALLOWED Links in Paper Notes

  1. •[[Project Name]] - links to files in Projects/
  2. •[[Paper Title]] - links to influential papers
    • •Link to papers even if they don't exist in vault yet (paper notes can be created later)
    • •MUST use exact, full paper titles in Title Case
    • •MUST format as wiki links with double brackets
    • •Example: [[Attention Is All You Need]] not "Attention is all you need"
    • •Example: [[BERT: Pre-Training of Deep Bidirectional Transformers for Language Understanding]]
    • •Example of future paper link: [[Representation Engineering - A Top-Down Approach to AI Transparency]]

❌ FORBIDDEN Links in Paper Notes

  • •[[Transformer Architecture]] - this is a concept, NOT allowed
  • •[[Attention Mechanism]] - this is a technique, NOT allowed
  • •[[Self-Supervised Learning]] - this is a method, NOT allowed
  • •[[BERT]] - this is a model name, NOT allowed (unless it's a paper title)
  • •[[Cross-Entropy Loss]] - this is a concept, NOT allowed
  • •Any link that is not explicitly a project or paper

How to Handle Technical Terms

Do NOT link them. Just write them as plain text.

Examples:

  • •❌ "The paper uses [[attention mechanisms]]"
  • •✅ "The paper uses attention mechanisms"
  • •❌ "They employ [[contrastive learning]]"
  • •✅ "They employ contrastive learning"

Exception: Only link if you're creating/referencing a PROJECT about that mechanism:

  • •✅ "Uses attention mechanisms → [[Scaling Laws for Attention Heads]]" (project)

Paper Access Rules

When searching for papers online:

  • •ALWAYS try to find the arXiv HTML version of the paper
  • •DO NOT download PDFs
  • •Use the arXiv HTML interface for reading and extracting information
  • •arXiv HTML URLs typically follow the pattern: https://arxiv.org/html/[paper-id]
  • •Only use PDFs as a last resort if no other option is available

Workflow

0. Read the template FIRST

MANDATORY FIRST STEP:

code
Use view tool on: Templates/Paper Note.md

Study the structure before creating the paper note.

1. Create paper note

  • •File name: exact paper title
  • •if present in paper title, exchange : for -
  • •Location: Reading/
  • •Copy template structure EXACTLY from Templates/Paper Note.md
  • •Fill each section with bullet points under the subsection prompts
  • •Do NOT remove subsection headings or prompts
  • •Link to existing projects immediately in "Linked Research Projects"
  • •Only propose new projects - don't create them yet

2. Fill template sections

Answer each subsection prompt with bullet points:

🌍 Background: Answer both subsection prompts ❓ Problem Statement: Answer all three subsection prompts 💡 Key Idea: Answer all three subsection prompts 🧭 High-Level Approach: Describe method/framework 🔬 Technical Details / Analysis: Answer all three subsection prompts 📊 Main Results / Observations: List findings 🧩 Interpretation: Answer both subsection prompts ⚠️ Limitations / Open Questions: List items 🔗 Connections to Other Work: Fill three subsections with [[Paper Title]] wiki links

  • •Link to ALL influential papers mentioned or referenced in the current paper
  • •Link even if paper notes don't exist in vault yet (they will be added when those papers are read)
  • •MUST use exact, full paper titles in Title Case
  • •MUST format as wiki links: [[Title]] not plain text
  • •Extract titles from paper references/citations when available 🚀 Relevance for My Research: Answer two prompts + add project links

CRITICAL: Write technical details as plain text. Do NOT create wiki links for concepts, methods, or techniques.

3. Identify existing projects and propose new ones

Part A: Link to existing projects immediately

  • •Search for existing projects in Projects/ that relate to the paper
  • •Add links to these existing projects in the paper note under "Linked Research Projects"
  • •No user approval needed for linking to existing projects
  • •Note: Reciprocal links (project → paper) will be added in step 4

Part B: Propose new projects (requires user approval)

CRITICAL: Ground proposals in the paper itself, not inferred extensions

Extract ideas directly from the paper's content:

  • •Explicit open questions the paper identifies (e.g., "future work", "unclear", "remains to be seen")
  • •Limitations the authors acknowledge
  • •Unexplained observations or surprising results mentioned in the paper
  • •Assumptions stated but not tested
  • •Gaps the paper identifies in prior work
  • •Follow-up experiments the paper suggests

DO NOT infer extensions beyond what the paper discusses. If the paper doesn't mention it, don't propose it.

Before creating ANY new project files:

  1. •Re-read the paper's "Limitations / Open Questions" section you filled in step 2
  2. •For each open question or limitation that could be a standalone project:
    • •Proposed project title (describes the idea, grounded in paper content)
    • •Quote or paraphrase from the paper showing where this question/gap appears
    • •1-2 sentence description of what it would explore
    • •Note if it's related to any existing project
  3. •Ask the user: "Should I create project files for these, or would you like to select specific ones?"
  4. •Wait for user response
  5. •Only create the approved new projects

Project title examples:

  • •Detecting Representation Drift During Fine-Tuning
  • •Preventing Emergent Misalignment via Gradient Monitoring

For each approved new project:

  • •create a new file in Projects/
  • •use Templates/Project.md as template
  • •status: seed
  • •add 1–3 bullet points minimum
  • •link the current paper under Relevant Papers

4. Create approved new projects and finalize bidirectional links

After receiving user approval, create the new project files:

  • •Create only the approved new projects in Projects/
  • •Use Templates/Project.md as template
  • •Fill with the descriptions you prepared
  • •Link the current paper under Relevant Papers in each project

CRITICAL: Bidirectional linking for existing projects

For every project linked from the paper note (both existing and newly created):

  1. •Open the project note in Projects/
  2. •Locate the "Relevant Papers" section
  3. •Add a wiki link to the paper note if it's not already there:
    • •Format: [[Paper Title]] (the paper note file name)
    • •Use Title Case with the exact paper title
    • •Place it in the "Relevant Papers" section
  4. •Save the project note

This ensures the graph remains consistent: if paper → project link exists, then project → paper link must also exist.

Then update the paper note:

  • •Add newly created project links to "Linked Research Projects" (existing projects should already be linked from step 1)
  • •Ensure paper links in "🔗 Connections to Other Work" subsections are complete
  • •CRITICAL: Use exact paper title in Title Case when linking to papers
  • •CRITICAL: Format paper references as wiki links: [[Paper Title]] not plain text
  • •If you don't know the exact title, use a descriptive title in Title Case
  • •Examples:
    • •✅ [[Sparse Autoencoders Find Highly Interpretable Features in Language Models]]
    • •✅ [[Concept Bottleneck Models]]
    • •❌ "Bricken et al. 2023" (not a wiki link)
    • •❌ [[sparse autoencoders]] (not title case, too generic)

VERIFY: Every [[link]] in the paper note is either:

  1. •A file in Projects/ (project note) - appears under "Linked Research Projects"
  2. •A paper title as wiki link - appears under "Connections to Other Work" as [[Title Case Paper Title]]
    • •Paper notes may not exist in vault yet, but will be added when those papers are read
    • •Use exact, full paper titles from references

5. Minimal quality check

Before finishing:

  • •ALL template sections present with emojis
  • •ALL subsection prompts (### questions) present
  • •Paper note contains ≥ 5 internal links (ONLY to projects/papers)
  • •At least one project note created or reused
  • •No paragraph longer than 3 bullets
  • •VERIFY: Every wiki link is to a file in Projects/ or Reading/
  • •No concept links (attention, transformers, etc.) - only plain text

Output Style

  • •bullet points only
  • •fragments preferred
  • •dense information
  • •no narrative text
  • •preserve ALL template structure, emojis, and subsection prompts
  • •technical terms as plain text, NOT wiki links
  • •links ONLY to projects (Projects/) or papers (Reading/)
  • •don't include : in file names. Exchange : always with -

Goal

Convert reading into:

  • •explicit mechanisms
  • •reusable research ideas
  • •connected project graph
  • •long-term synthesis potential
  • •properly structured notes following template exactly

Important workflow:

  • •Link to existing projects immediately without asking
  • •Propose new projects and get user approval before creating them

A paper note without linked projects is considered incomplete. A paper note that doesn't follow the template structure is considered invalid.

Self-Check Before Completing

Template structure:

  1. •Did I read Templates/Paper Note.md first? ✅
  2. •Are ALL emoji section headers present? ✅
  3. •Are ALL subsection prompts (### questions) present? ✅
  4. •Did I answer each subsection separately? ✅

Links: For EVERY [[link]] in the paper note:

  1. •Is this link pointing to a file in Projects/? ✅
  2. •Is this link pointing to a file in Reading/? ✅
  3. •Is this link a concept/method/technique? ❌ REMOVE
  4. •For paper links: Is it in Title Case with wiki link brackets? ✅
  5. •For paper links: Did I use the full paper title, not "Author et al."? ✅

Bidirectional linking verification:

  1. •For each project linked in the paper note:
    • •Did I add/verify the reciprocal link from project → paper? ✅
    • •Does the project's "Relevant Papers" section include this paper? ✅
  2. •All paper-project relationships are now bidirectional ✅

If uncertain whether something should be a link: Don't link it. Use plain text.