Literature survey

Literature Survey Loop

A search → extract → map → expand loop that builds an evidence/contradiction matrix and stops at saturation. The artifact is the matrix (claims × sources, with each source's stance); the feedback signal is how many new, matrix-changing sources a round adds — you keep expanding until that falls below <min_new> for <patience> rounds. Unlike a one-shot summary, the loop deliberately hunts contradictions and gaps and keeps pulling threads until the picture stops changing.

The discipline: every cell — a source's stance on a claim — is backed by a verbatim snippet from a real retrieval. The value is not a tidy narrative; it is an honest map of where the literature agrees, disagrees, and is silent.

When to use

Use this for a multi-source survey of a question where the deliverable is a structured map of the evidence, not a paragraph. Default: run the full expand→admit→map loop below until saturation. Escape hatch: if the user wants only a quick scan, run round 0 (seed) alone and hand back the seed matrix. Not for grading a written proposal against the literature, and not for proposing new hypotheses.

Setup

Resolve bindings interactively. If loop.run.yaml exists in the working dir, load it, confirm the values in one line, and skip to the loop. Otherwise: on Claude Code (the AskUserQuestion tool is available) infer a likely value for each binding and present it as the recommended option; on other hosts ask each as a quoted plain-text prompt. Then write loop.run.yaml (format: examples/run.example.yaml) and confirm every value plus the live/degraded literature tier before creating any other files.

binding	meaning	default	how to infer
<question>	the survey question/topic, with any scope (years, sub-fields, inclusion criteria)	—	ask the user; restate the scope back for confirmation
<eval_scale>	depth per round (low/medium/high, see below)	medium	—
<matrix>	structured output matrix (validates schemas/matrix.schema.json); survey.md written alongside	<sandbox_root>/matrix.json	—
<sandbox_root>	where the matrix, survey.md, ledger, and lit cache live	./sandbox	—
<budget>	max rounds	6	—
<patience>	stop after this many consecutive "dry" rounds	2	—
<min_new>	saturation threshold — a round is "dry" if it adds fewer than this many new, matrix-changing sources	2	—

Evaluation depth dial (<eval_scale> caps per round — queries · citation-walks · fulltext reads · new-source admit cap):

preset	queries · walks	fulltext reads	new-source cap
low	2 · 0	0 (snippet/abstract only)	~6
medium (recommended)	4 · 1	1	~10
high	6 · ≥2	3	~16

Literature toolchain. Paper search goes through the sibling literature-search skill: resolve <lit_skill_dir> (it installs as a sibling, default ~/.claude/skills/literature-search/), <lit_py> = python3, and <lit> = <lit_skill_dir>/tools/lit_search.py (note the tools/ segment); append --cache-dir <sandbox_root>/literature/.cache after a subcommand to reuse the cache. Subcommands used here: search "<q>" (discover sources), snippet "<q>" (verbatim passage = the evidence for a cell), cite <paperId> --direction references|citations|recommend (walk the citation graph), fulltext <arxivId> (deep-read one key paper). Confirm <lit> --help works at setup; because this loop is literature retrieval, do not silently proceed if the skill is missing — tell the user and either install it or degrade all retrieval to WebSearch/WebFetch (no ranked snippets or citation-graph expansion), tagging that evidence source:"web".

S2 key (optional, never block). A free S2_API_KEY makes snippet/cite reliable. Run <lit> keys --init, have the user fill the printed keys.env themselves, never paste secrets into chat; a missing key just degrades to the keyless pool → WebSearch. Record presence (booleans only) in loop.run.yaml.

The loop

matrix = sources + claims + gaps (starts empty). dry = consecutive dry rounds (starts 0). <N> starts at 0.

Copy this checklist and tick items off:

• Round 0 — seed. Decompose <question> into sub-topics; run one <lit> search each, admit the most relevant sources, extract each one's key claim(s) into the matrix with a verbatim snippet, note obvious gaps.
• Expand. Pick the least-covered sub-topics and open contradictions/gaps; run new <lit> search queries and walk the citation graph (<lit> cite) from the 1-2 most central papers. Honor the <eval_scale> caps.
• Admit & extract. Dedupe against existing sources (by title/id); for each genuinely new source extract its key claim(s) + a verbatim snippet.
• Map. For each claim, record where each relevant source stands — supports / contradicts / qualifies — with its snippet; set is_contested when sources both support and contradict; add newly-exposed gaps.
• Saturation check. Count new, matrix-changing sources this round: dry += 1 if fewer than <min_new>, else dry = 0. Steer the next round at whatever is still thin.
• Log one ledger row; N = N + 1; stop on saturation (dry == <patience>) or <budget>.

On stop, write <matrix> (validates schemas/matrix.schema.json) and survey.md — a synthesis organized as consensus (well-supported claims), disputes (the contested claims and who is on each side), and gaps (open questions), each citing its sources, plus an honest coverage note naming which sub-topics are well covered and which are thin.

The matrix is the schema-validated artifact; a compact generic instance (see schemas/matrix.schema.json):

{
  "question": "<question>",
  "sources": [{"key": "S1", "title": "...", "source": "s2", "id": "...", "year": 2022}],
  "claims": [{
    "claim_id": "C1", "statement": "...", "is_contested": true,
    "positions": [
      {"source_key": "S1", "stance": "supports",    "snippet": "verbatim passage ..."},
      {"source_key": "S3", "stance": "contradicts",  "snippet": "verbatim passage ..."}
    ]
  }],
  "gaps": ["open question the survey surfaced"]
}

source ∈ {s2, arxiv, web}; stance ∈ {supports, contradicts, qualifies}.

Ledger

<sandbox_root>/ledger.tsv, tab-separated, never commas in the text. Header:

round	queries	new_sources	total_sources	new_claims	contested	dry

Example:

round	queries	new_sources	total_sources	new_claims	contested	dry
0	4	7	7	9	1	0
1	5	5	12	4	2	0
2	4	1	13	0	2	1
3	4	0	13	0	2	2

Report the new-sources trajectory so the reader sees saturation actually happen, not just the final count.

Constraints

• Never fabricate. Every source, claim snippet, and stance comes from a real <lit> / WebFetch retrieval that round, and snippets are verbatim; on {"error","fallback"}, use WebSearch/WebFetch and tag the evidence source:"web" — the verbatim-snippet rule is what makes the matrix trustworthy.
• Map disagreement, do not smooth it. When sources conflict, record the contradiction explicitly (is_contested, both snippets); surfacing disputes is the point, not picking a winner.
• Saturation is measured, not guessed — stop because new-sources-per-round actually fell below <min_new>, and report coverage honestly rather than implying completeness the search did not reach.
• Dedupe sources so "new sources" counts real additions, not re-finds of the same paper.
• No installs — the sibling literature-search skill is stdlib-only; never print or commit API keys (keys.env stays gitignored at the project root). The sandbox is self-contained — no ../ escapes.
• Do not pause the loop to ask whether to continue; run until saturation, patience, or budget.

Stops

The loop stops on the first of:

• Saturation — dry == <patience> (each of those rounds added fewer than <min_new> new sources).
• Budget — N == <budget> rounds reached.

Always end with: the <matrix> path, the synthesis (consensus / disputes / gaps), the source count and new-sources trajectory from ledger.tsv showing saturation, and the coverage note naming the thin spots.