deep-research

这段内容是审核时保存的快照。外部来源才是完整且最新的版本。

---
name: deep-research
description: Conduct systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report. Output is organized by phase for clarity.
argument-hint: [topic]
---

# Deep Research Skill

## Trigger

Activate this skill when the user wants to:
- "Research a topic", "literature review", "find papers about", "survey papers on"
- "Deep dive into [topic]", "what's the state of the art in [topic]"
- Uses `/research <topic>` slash command

## Overview

This skill conducts systematic academic literature reviews in 6 phases, producing structured notes, a curated paper database, and a synthesized final report. Output is organized **by phase** for clarity.

**Installation**: `~/.claude/skills/deep-research/` — scripts, references, and this skill definition.
**Output**: `.//Users/lingzhi/Code/deep-research-output/{slug}/` relative to the current working directory.

## CRITICAL: Strict Sequential Phase Execution

**You MUST execute all 6 phases in strict order: 1 → 2 → 3 → 4 → 5 → 6. NEVER skip any phase.**

This is the single most important rule of this skill. Violations include:
- ❌ Jumping from Phase 2 to Phase 5/6 (skipping Deep Dive and Code)
- ❌ Writing synthesis or report before completing Phase 3 deep reading
- ❌ Producing a final report based only on abstracts/titles from search results
- ❌ Combining or merging phases (e.g., doing "Phase 3-5 together")

### Phase Gate Protocol

Before starting Phase N+1, you MUST verify that Phase N's **required output files** exist on disk. If they don't exist, you have NOT completed that phase.

| Phase | Gate: Required Output Files |
|-------|---------------------------|
| 1 → 2 | `phase1_frontier/frontier.md` exists AND contains ≥10 papers |
| 2 → 3 | `phase2_survey/survey.md` exists AND `paper_db.jsonl` has 35-80 papers |
| 3 → 4 | `phase3_deep_dive/selection.md` AND `phase3_deep_dive/deep_dive.md` exist AND deep_dive.md contains detailed notes for ≥8 papers |
| 4 → 5 | `phase4_code/code_repos.md` exists AND contains ≥3 repositories |
| 5 → 6 | `phase5_synthesis/synthesis.md` AND `phase5_synthesis/gaps.md` exist |

**After completing each phase, print a phase completion checkpoint:**
```
✅ Phase N complete. Output: [list files written]. Proceeding to Phase N+1.
```

### Why Every Phase Matters

- **Phase 3 (Deep Dive)** is where you actually READ papers — without it, your synthesis is superficial and based only on abstracts
- **Phase 4 (Code & Tools)** grounds the research in practical implementations — without it, you miss the open-source ecosystem
- **Phase 5 (Synthesis)** requires deep knowledge from Phase 3 — you cannot synthesize papers you haven't read
- **Phase 6 (Report)** assembles content from ALL prior phases — it should cite specific findings from Phase 3 notes

## Paper Quality Policy

**Peer-reviewed conference papers take priority over arXiv preprints.** Many arXiv papers have not undergone peer review and may contain unverified claims.

### Source Priority (highest to lowest)
1. **Top AI conferences**: NeurIPS, ICLR, ICML, ACL, EMNLP, NAACL, AAAI, IJCAI, CVPR, KDD, CoRL
2. **Peer-reviewed journals**: JMLR, TACL, Nature, Science, etc.
3. **Workshop papers**: NeurIPS/ICML workshops (lower bar but still reviewed)
4. **arXiv preprints with high citations**: Likely high-quality but unverified
5. **Recent arXiv preprints**: Use cautiously, note "preprint" status explicitly

### When to Use arXiv Papers
- As **supplementary** evidence alongside peer-reviewed work
- For **very recent** results (< 3 months old) not yet at conferences
- When a peer-reviewed version doesn't exist yet — note `(preprint)` in citations
- For **survey/review** papers (these are useful even without peer review)

## Search Tools (by priority)

### 1. paper_finder (primary — conference papers only)
**Location**: `/Users/lingzhi/Code/documents/tool/paper_finder/paper_finder.py`

Searches ai-paper-finder.info (HuggingFace Spa