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deer-flow/skills/public/systematic-literature-review/templates/apa.md
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KKK 16aa51c9b3 feat(skills): add systematic-literature-review skill for multi-paper SLR workflows (#2032)
* feat(skills): add systematic-literature-review skill for multi-paper SLR workflows

Adds a new skill that produces a structured systematic literature review (SLR)
across multiple academic papers on a topic. Addresses #1862 with a pure skill
approach: no new tools, no architectural changes, no new dependencies.

Skill layout:
- SKILL.md — 4+1 phase workflow (plan, search, extract, synthesize, present)
- scripts/arxiv_search.py — arXiv API client, stdlib only, with a
  requests->urllib fallback shim modeled after github-deep-research's
  github_api.py
- templates/{apa,ieee,bibtex}.md — citation format templates selected
  dynamically in Phase 4, mirroring podcast-generation's templates/ pattern

Design notes:
- Multi-paper synthesis uses the existing `task` tool to dispatch extraction
  subagents in parallel. SKILL.md's Phase 3 includes a fixed decision table
  for batch splitting to respect the runtime's MAX_CONCURRENT_SUBAGENTS = 3
  cap, and explicitly tells the agent to strip the "Task Succeeded. Result: "
  prefix before parsing subagent JSON output.
- arXiv only, by design. Semantic Scholar and PubMed adapters would push the
  scope toward a standalone MCP server (see #933) and are intentionally out
  of scope for this skill.
- Coexists with the existing `academic-paper-review` skill: this skill does
  breadth-first synthesis across many papers, academic-paper-review does
  single-paper peer review. The two are routed via distinct triggers and
  can compose (SLR on many + deep review on 1-2 important ones).
- Hard upper bound of 50 papers, tied to the Phase 3 concurrency strategy.
  Larger surveys degrade in synthesis quality and are better split by
  sub-topic.

BibTeX template explicitly uses @misc for arXiv preprints (not @article),
which is the most common mistake when generating BibTeX for arXiv papers.

arxiv_search.py was smoke-tested end-to-end against the live arXiv API with
two query shapes (relevance sort, submittedDate sort with category filter);
all returned JSON fields parse correctly (id normalization, Atom namespace
handling, URL encoding for multi-word queries).

* fix(skills): prevent LLM from saving intermediate search results to file

Adds an explicit "do not save" instruction at the end of Phase 2.
Observed during Test 1 with DeepSeek: the model saved search results
to a markdown file before proceeding to Phase 3, wasting 2-3 tool call
rounds and increasing the risk of hitting the graph recursion limit.
The search JSON should stay in context for Phase 3, not be persisted.

* fix(skills): use relevance+start-date instead of submittedDate sorting

Test 2 revealed that arXiv's submittedDate sorting returns the most
recently submitted papers in the category regardless of query relevance.
Searching "diffusion models" with sortBy=submittedDate in cs.CV returned
papers on spatial memory, Navier-Stokes, and photon-counting CT — none
about diffusion models. The LLM then retried with 4 different queries,
wasting tool calls and approaching the recursion limit.

Fix: always sort by relevance; when the user wants "recent" papers,
combine relevance sorting with --start-date to constrain the time window.
Also add an explicit "run the search exactly once" instruction to prevent
the retry loop.

* fix(skills): wrap multi-word arXiv queries in double quotes for phrase matching

Without quotes, `all:diffusion model` is parsed by arXiv's Lucene as
`all:diffusion OR model`, pulling in unrelated papers from physics
(thermal diffusion) and other fields. Wrapping in double quotes forces
phrase matching: `all:"diffusion model"`.

Also fixes date filtering: the previous bug caused 2011 papers to appear
in results despite --start-date 2024-04-09, because the unquoted query
words were OR'd with the date constraint.

Verified: "diffusion models" --category cs.CV --start-date 2024-04-09
now returns only relevant diffusion model papers published after April
2024.

* fix(skills): add query phrasing guide and enforce subagent delegation

Two fixes from Test 2 observations with DeepSeek:

1. Query phrasing: add a table showing good vs bad query examples.
   The script wraps multi-word queries in double quotes for phrase
   matching, so long queries like "diffusion models in computer vision"
   return 0 results. Guide the LLM to use 2-3 core keywords + --category
   instead.

2. Subagent enforcement: DeepSeek was extracting metadata inline via
   python -c scripts instead of using the task tool. Strengthen Phase 3
   to explicitly name the task tool, say "do not extract metadata
   yourself", and explain why (token budget, isolation). This is more
   direct than the previous natural-language-only approach while still
   providing the reasoning behind the constraint.

* fix(skills): strengthen search keyword guidance and subagent enforcement

Address two issues found during end-to-end testing with DeepSeek:

1. Search retry: LLM passed full topic descriptions as queries (e.g.
   "diffusion models in computer vision"), which returned 0 results due
   to exact phrase matching and triggered retries. Added explicit
   instruction to extract 2-3 core keywords before searching.

2. Subagent bypass: LLM used python -c to extract metadata instead of
   dispatching via task tool. Added explicit prohibition list (python -c,
   bash scripts, inline extraction) with  markers for clarity.

* fix(skills): address Copilot review feedback on SLR skill

- Fix legacy arXiv ID parsing: preserve archive prefix for pre-2007
  papers (e.g. hep-th/9901001 instead of just 9901001)
- Fix phase count: "four phases" -> "five phases"
- Add subagent_enabled prerequisite note to SKILL.md Notes section
- Remove PR-specific references ("PR 1") from ieee.md and bibtex.md
  templates, replace with workflow-scoped wording
- Fix script header: "stdlib only" -> "no additional dependencies
  required", fix relative path to github_api.py reference
- Remove reference to non-existent docs/enhancement/ path in header

* Apply suggestions from code review

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
2026-04-10 08:54:28 +08:00

6.0 KiB

APA 7th Edition Citation Template

Use this template when the user requests APA format, or when they do not specify a format. APA 7th is the default for social sciences and most CS journals outside of IEEE venues.

Citation Format Rules

In-text citations

  • Single author: (Vaswani, 2017) or Vaswani (2017) showed that...
  • Two authors: (Vaswani & Shazeer, 2017) — use & inside parentheses, "and" in running text.
  • Three or more authors: (Vaswani et al., 2017) — use et al. from the first citation onward (APA 7th changed this from APA 6th).
  • Multiple citations: (Vaswani et al., 2017; Devlin et al., 2018) — alphabetical order, separated by semicolons.

Reference list entry for arXiv preprints

arXiv papers are preprints, not formally published articles. Cite them as preprints with the arXiv identifier:

Author, A. A., Author, B. B., & Author, C. C. (Year). Title of the paper. arXiv. https://arxiv.org/abs/ARXIV_ID

Real example (from paper metadata {id: "1706.03762", title: "Attention Is All You Need", authors: ["Ashish Vaswani", "Noam Shazeer", "Niki Parmar", "Jakob Uszkoreit", "Llion Jones", "Aidan N. Gomez", "Łukasz Kaiser", "Illia Polosukhin"], published: "2017-06-12"}):

Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A. N., Kaiser, Ł., & Polosukhin, I. (2017). Attention is all you need. arXiv. https://arxiv.org/abs/1706.03762

Formatting rules:

  • Author names: LastName, FirstInitial. (middle initial optional). Join with commas; last author gets an &.
  • Year: the published field's year, in parentheses.
  • Title: sentence case (only first word and proper nouns capitalized). Italicize titles in typeset output; in plain markdown, leave plain.
  • Source: the literal word arXiv, then the full abs URL.
  • No DOI unless the paper has also been published in a venue with a DOI. arXiv alone uses the URL.

Special cases

  • Up to 20 authors: list all of them separated by commas, with & before the last.
  • 21 or more authors: list the first 19, then ..., then the final author.
  • No DOI and no URL: not possible for arXiv papers; always use the abs_url from the paper metadata.

Report Structure

Follow this structure verbatim when writing the SLR report body. Fill in content from your Phase 3 extraction and Phase 4 synthesis.

# Systematic Literature Review: <Topic>

**Date**: <YYYY-MM-DD>
**Papers surveyed**: <N>
**Scope**: <arXiv search query, category, time window>
**Citation format**: APA 7th edition

## Executive Summary

<3-5 sentences summarizing the state of the literature on this topic. What do the surveyed papers collectively tell us? What is the shape of the field? Avoid listing papers — synthesize.>

## Methodology

This review surveyed <N> arXiv papers retrieved on <YYYY-MM-DD> using the query `<query>`<, filtered to category <cat>><, published between <start_date> and <end_date>>. Papers were sorted by <relevance | submission date> and the top <N> were included. Metadata extraction (research question, methodology, key findings, limitations) was performed by language-model agents, with cross-paper synthesis performed by the lead agent.

**Limitations of this review**: arXiv preprints are not peer-reviewed; some included papers may not reflect their final published form. Coverage is limited to arXiv — papers published directly in venues without arXiv preprints are not represented.

## Themes

<3-6 thematic sections. Each theme is a recurring research direction, problem framing, or methodological approach across the surveyed papers.>

### Theme 1: <Theme name>

<2-4 paragraphs describing this theme. Cite papers inline as you discuss them, e.g. "Vaswani et al. (2017) introduced X, while subsequent work (Devlin et al., 2018; Liu et al., 2019) extended it to Y." Do not just list papers — describe the intellectual thread that connects them.>

### Theme 2: <Theme name>

<...>

## Convergences and Disagreements

**Convergences**: <findings that multiple papers agree on — e.g. "Most surveyed papers agree that X is necessary, citing evidence from Y and Z.">

**Disagreements**: <where papers reach different conclusions — e.g. "Vaswani et al. (2017) argue that X, while Dai et al. (2019) find the opposite under condition Y.">

## Gaps and Open Questions

<What the collective literature does not yet address. Pull from the "limitations" field of your Phase 3 extraction and identify patterns — if 5 papers all mention the same missing piece, that is a gap worth flagging.>

## Per-Paper Annotations

<One subsection per paper, ordered by year then first author. Each subsection is a mini-summary of that paper's contribution.>

### Vaswani et al. (2017)

**Research question**: <1 sentence from Phase 3 metadata>
**Methodology**: <1-2 sentences>
**Key findings**:
- <bullet>
- <bullet>
- <bullet>
**Limitations**: <1-2 sentences>

### <Next paper>

<...>

## References

<Alphabetical list by first author's last name, APA 7th format as described above.>

Devlin, J., Chang, M.-W., Lee, K., & Toutanova, K. (2018). BERT: Pre-training of deep bidirectional transformers for language understanding. arXiv. https://arxiv.org/abs/1810.04805

Vaswani, A., Shazeer, N., Parmar, N., Uszkoreit, J., Jones, L., Gomez, A. N., Kaiser, Ł., & Polosukhin, I. (2017). Attention is all you need. arXiv. https://arxiv.org/abs/1706.03762

<... more entries, one per paper ...>

Quality checks before finalizing

Before saving the report, verify:

  • Every paper in the surveyed set appears both in "Per-Paper Annotations" and in "References".
  • Every in-text citation matches a reference entry (no dangling citations).
  • Authors are formatted LastName, FirstInitial. — not FirstName LastName.
  • Years are in parentheses inline, and at the start of reference entries.
  • Titles are in sentence case in references (only first word + proper nouns capitalized).
  • arXiv URLs use the abs_url form (https://arxiv.org/abs/...), not pdf_url.
  • References are alphabetized by first author's last name.