consensus-domains

Research

Multi-method consensus over spatial-domains. Fans out 5 methods in parallel, computes a SACCELERATOR-style base-clustering ranking, runs typed consensus (kmode / weighted / LCA), and emits a verified consensus report with the mandatory A-path banner per ADR 0010.

QUICK START

How to use this skill

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Source SKILL.md: https://github.com/TianGzlab/OmicsClaw/blob/HEAD/skills/spatial/consensus-domains/SKILL.md

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consensus-domains

When to use

The user has a preprocessed spatial AnnData (typically already QC'd via spatial-preprocess) and wants a more trustworthy tissue-domain assignment than any single method can produce — because the user knows single-method results disagree on cancer / non-standard tissues, or because the analysis is going to drive a downstream decision (cell-type deconvolution, region-specific DE, paper figure).

This skill fans out spatial-domains over N method choices, computes a typed statistical consensus, and surfaces the cross-method disagreement explicitly. It does NOT replace spatial-domains; it wraps it.

Inputs & Outputs

Input	Format	Required
Preprocessed AnnData	`--input <preprocessed.h5ad>` (PCA + spatial graph)	yes
Output directory	`--output <dir>`	yes
Member list	`--members banksy,graphst,sedr,leiden,spagcn`	no (defaults to LLM-curated 5)
Run ALL eligible methods	`--all`	no (slower; SACCELERATOR-style benchmark mode)
Target cluster count	`--n-clusters 7`	no (defaults to median across members)
Pre-run plan confirmation	`--confirm-plan`	no (default off)
Non-interactive BC picker	`--non-interactive`	no (forces top-K by score)
Score weights	`--alpha 0.6 --beta 0.4`	no (ADR 0011 defaults)
Class-imbalance cap	`--max-class-frac 0.8`	no
LLM judge veto/reweight	`--llm-judge`	no (default deterministic)
Operator	`--operator {kmode,weighted,lca}`	no (default `kmode`)
Seed	`--seed 0`	no
Per-member timeout (s)	`--timeout 600`	no
Concurrency cap	`--max-parallel 4`	no

Output	Path	Notes
Verified consensus labels	`consensus_labels.tsv`	columns `observation,consensus_<operator>`
Per-member labels (raw)	`member_<name>/figure_data/spatial_*.csv`	passed through from spatial-domains
Cross-method NMI matrix	`cross_method_nmi.csv`	square matrix per member
Composite member scores	`member_scores.csv`	ADR 0011 schema
Markdown report	`report.md`	starts with `[A: Verified consensus]` (non-configurable)
Plan + audit trail	`plan.json`	LLM rationale + chosen operator + filtered members

Flow

Plan — runtime/consensus/plan.propose_members reads skills/spatial/spatial-domains/parameters.yaml param_hints, queries the evaluation-chair LLM (or falls back deterministically), produces N PlannedMember entries.
Fan out — runtime/consensus/team.run_team invokes omicsclaw.skill.runner.run_skill("spatial-domains", ...) per member with max_parallel = min(N, cpu_count//2, 4) and a 600 s per-member timeout. cancel_event is propagated through.
Score — runtime/consensus/scoring.score_all_members ranks survivors by composite alpha * cross_NMI + beta * mean_local_purity with the max_class_frac > 0.8 hard filter.
BC pick — on the CLI surface in interactive mode, prompt the user with the top-K-by-score default; on Desktop/Channel surfaces (or --non-interactive), accept the default.
Consensus — invoke the chosen operator (kmode / weighted / lca) on the selected base clusterings.
Report — write report.md starting with the mandatory ADR 0010 banner; persist plan.json for audit; ready for graph-memory storage under analysis://typed/<run_id>.

Gotchas

A path is allowed to fail loudly. If fewer than 2 members survive the fan-out, this skill raises InsufficientSurvivorsError and does NOT silently downgrade to narrative consensus. Re-run with --members adjusted or fall back to the dedicated narrative skill (when shipped).
Banner is non-configurable. The [A: Verified consensus] header is enforced by runtime/consensus/dispatch.output_banner. Do not edit report.md to strip it before distribution.
--n-clusters defaults to the median across members, not 7. Override only when you have prior k from histology / known anatomy.
LCA requires R + diceR. When unavailable, the skill prints an installation hint and exits non-zero rather than silently switching operators. Pass --operator kmode to bypass.
requires_preprocessed: true — the underlying spatial-domains members expect obsm["X_pca"] and obsm["spatial"] populated. Run spatial-preprocess first.

Key CLI

# Minimal interactive run (CLI surface) — LLM picks 5, you confirm BCs
oc run consensus-domains --input preprocessed.h5ad --output out/

# Non-interactive (server / scripted)
oc run consensus-domains --input preprocessed.h5ad --output out/ \
  --non-interactive

# Explicit members + weighted operator
oc run consensus-domains --input preprocessed.h5ad --output out/ \
  --members banksy,graphst,sedr,leiden,spagcn \
  --operator weighted --n-clusters 7

# SACCELERATOR-style benchmark (run ALL eligible methods)
oc run consensus-domains --input preprocessed.h5ad --output out/ --all

Pointers

ADR 0010 — runtime layer architecture
ADR 0011 — scoring + evaluation protocol
omicsclaw/runtime/consensus/ — runtime module
examples/consensus_benchmark/ — DLPFC 151673 hero benchmark