Autosci Survey

/survey

Generate a Related Work section ready for direct use in a paper, based on existing wiki knowledge. Draw material from wiki/papers/, concepts/, topics/; group by research direction (not paper-by-paper listing). End each group with a statement of how it differs from this work. Citations follow citation-verification.md; writing follows academic-writing.md Related Work rules. Supports LaTeX and Markdown output formats.

Inputs

• query: one of:
  • research question description (free text, e.g. "parameter-efficient fine-tuning for LLMs")
  • list of idea slugs (from wiki/ideas/, used to organize related work around specific ideas)
  • path to PAPER_PLAN.md (extract Related Work section definition from it)
• --format (optional, default latex): output format
  • latex: \cite{key} citations, embeddable directly in a paper
  • markdown: [[slug]] wikilink citations, for wiki archiving
• --max-papers (optional, default 30): maximum number of papers to cite

Outputs

• wiki/outputs/related-work-{slug}-{date}.md — Related Work text (archived)
• wiki/graph/edges.jsonl — derived_from edges (if a new output is created)
• wiki/log.md — appended log entry
• Terminal output — Related Work body text (for direct copy-paste)

Wiki Interaction

Reads

• wiki/papers/*.md — Problem & Context, Key idea, Experiment & Results, Related, My take
• wiki/concepts/*.md — Definition, Variants, Comparison, Known limitations
• wiki/topics/*.md — Overview, Timeline, Open problems, Seminal works
• wiki/ideas/*.md — Hypothesis, Motivation, origin_gaps (if input is idea slugs)
• wiki/methods/*.md — Mechanism, Procedure, source_papers (when ideas reference methods)
• wiki/index.md — content catalog, filtered by importance
• wiki/graph/context_brief.md — global context
• wiki/graph/edges.jsonl — inter-paper semantic relationships (same_problem_as, similar_method_to, builds_on, challenges)
• .claude/skills/shared-references/academic-writing.md — Related Work writing rules
• .claude/skills/shared-references/citation-verification.md — citation discipline

Writes

• wiki/outputs/related-work-{slug}-{date}.md — archived file
• wiki/graph/edges.jsonl — derived_from edges
• wiki/log.md — appended operation log

Graph edges created

• derived_from: related-work output → source papers

Workflow

Precondition: confirm the working directory is the wiki project root (the directory containing wiki/, raw/, tools/).

Step 1: Locate Relevant Knowledge

1. Parse input:
   • If free text: extract keywords; match against tags and titles in wiki/index.md
   • If idea slugs: read each idea's origin_gaps (concepts/topics) and walk to concepts.key_papers and topic seminal works to collect related papers; also read methods linked from the idea's ## Approach sketch and pull their source_papers
   • If PAPER_PLAN path: read the Related Work section's groupings and citations
2. Read wiki/graph/context_brief.md for global context
3. Read wiki/graph/edges.jsonl: extract inter-paper semantic relationships (same_problem_as, similar_method_to, builds_on, challenges)
4. Build candidate paper list:
   • Sort by importance descending from index.md
   • Rank by tags and domain match
   • Cap at --max-papers papers
5. If candidate papers < 5: warn "insufficient related papers; consider /ingest of more papers first"

Step 2: Deep-Read Related Pages

For each paper in the candidate list:

1. Read wiki/papers/{slug}.md: focus on Problem & Context, Key idea, Experiment & Results, My take
2. Read linked wiki/concepts/*.md: focus on Definition, Variants, Comparison
3. Read related wiki/topics/*.md: focus on Timeline, Open problems

Record for each paper:

• core contribution (one sentence)
• method category (which research direction it belongs to)
• relationship to this work (same problem / similar method / builds on / challenges)
• limitations (extracted from Limitations or My take)

Step 3: Thematic Grouping

Following the Related Work rules in shared-references/academic-writing.md:

1. Group by research direction (not paper-by-paper listing):
   • Extract natural groupings from wiki/topics/ and concepts/ classifications
   • 3–8 papers per group
   • Group headings describe research directions (e.g. "Parameter-Efficient Fine-Tuning"), not individual papers
2. Determine group order:
   • Broad to specific (major direction → sub-direction → most related methods)
   • Or chronological (foundational → development → recent)
3. Determine within-group order:
   • Ascending by year (show progression)
   • Important papers: 2–3 sentences; secondary papers: 1 sentence
4. Annotate each group's relationship to this work:
   • End each group with one sentence: "Unlike these approaches, our method..." or "We build upon X by..."

Step 4: Generate Paragraphs

Following shared-references/academic-writing.md:

1. One or two paragraphs per group:

   • Opening: background and importance of the direction
   • Body: expand on each paper's contribution in within-group order
   • Closing: positioning relative to this work (required)

2. Citation format:

   • --format latex: \cite{key}, key generated from citation-verification.md naming rules
   • --format markdown: [[slug]]

3. Writing standards:

   • No flat lists ("X did Y. Z did W.")
   • Each paragraph has a topic sentence
   • Use contrastive connectives ("While X focuses on..., Y addresses...")
   • No AI-signature vocabulary (see de-AI list in academic-writing.md)

4. De-AI polish:

   • Scan and replace AI-signature vocabulary
   • Vary sentence openings
   • Remove filler sentences

Step 5: BibTeX Preparation (--format latex only)

If output format is LaTeX, following shared-references/citation-verification.md:

1. Collect all \cite{key} citations
2. For each key, attempt to fetch BibTeX: DBLP → CrossRef → S2
3. Verified: record BibTeX
4. Unverified: mark [UNCONFIRMED]
5. Output list of BibTeX entries (can be appended to paper/references.bib)
6. Report citation coverage

Step 6: Archive

1. Generate slug:

   python3 tools/research_wiki.py slug "<query-keywords>"
   

2. Write archive file: Create wiki/outputs/related-work-{slug}-{date}.md:

   ---
   title: "Related Work: {topic}"
   type: related-work
   format: {latex|markdown}
   paper_count: {N}
   date_generated: YYYY-MM-DD
   ---
   

   Body is the complete Related Work text. If latex format: append BibTeX entries as an appendix.

3. Add graph edges:

   # output → each cited paper
   python3 tools/research_wiki.py add-edge wiki/ \
     --from "outputs/related-work-{slug}-{date}" --to "papers/{paper-slug}" \
     --type derived_from --evidence "Cited in related work section"
   

4. Append log:

   python3 tools/research_wiki.py log wiki/ \
     "survey | {topic} | {N} papers, {G} groups, format: {format}"
   

5. Terminal output: complete Related Work body text + citation coverage statistics

Constraints

• Only cite papers already in the wiki: do not fabricate citations; every \cite{} or [[slug]] must correspond to a page in wiki/papers/
• Group by theme, not as a flat list: each paragraph covers a research direction, not "Paper A did X. Paper B did Y."
• Every group must have a positioning sentence: state the relationship to this work (at the end — difference or inheritance)
• Warn when candidate papers < 5: prompt user to /ingest more papers first
• BibTeX follows citation-verification.md: do not generate from LLM memory (--format latex only)
• De-AI polish is mandatory: a polish pass must be applied after generation
• Archive to outputs/: do not directly modify wiki papers/concepts/topics pages
• Graph edges via tools/research_wiki.py: do not manually edit edges.jsonl

Error Handling

• Fewer than 3 wiki papers: error; suggest /ingest of enough papers first
• No matching papers: broaden search scope (relax tag matching); if still none, error
• All BibTeX fetches failed (latex format): use [UNCONFIRMED] placeholders; report count
• PAPER_PLAN format mismatch: ignore plan's grouping suggestions; use automatic grouping
• Slug conflict: append date suffix

Dependencies

Tools（via Bash）

• python3 tools/research_wiki.py slug "<title>" — generate slug
• python3 tools/research_wiki.py add-edge wiki/ ... — add graph edge
• python3 tools/research_wiki.py log wiki/ "<message>" — append log
• python3 tools/fetch_s2.py search "<title>" — BibTeX fallback (S2 search)

MCP Servers

• None (survey does not require Review LLM; use /review --focus writing for separate review)

Claude Code Native

• Read — read wiki pages
• Glob — find ideas, methods, concepts, topics, papers
• WebFetch — DBLP / CrossRef BibTeX fetch (--format latex only)

Shared References

• .claude/skills/shared-references/academic-writing.md — Related Work writing rules + de-AI polish
• .claude/skills/shared-references/citation-verification.md — BibTeX fetch and [UNCONFIRMED] protocol

Called by

• /paper-draft Step 3 (Related Work section can be delegated to this skill)
• Manual user invocation