research-pipeline

Full Research Pipeline: Idea → Experiments → Submission

⏱ External cadence: non-judgmental heartbeat only. An overnight /loop /

CronCreate heartbeat may wake, detect a stalled phase (no progress, dead

process, blocked on a freed resource) and nudge it forward — it may NEVER

decide the work is good (paper good enough, proof holds, claim supported).

Every such verdict stays on its own skill's internal cadence and terminates in

the cross-model jury. A heartbeat may say "keep going," never "good enough."

See

[shared-references/external-cadence.md](../shared-references/external-cadence.md)

(overnight-pipeline rule).

End-to-end autonomous research workflow for: $ARGUMENTS

Constants

• AUTO_PROCEED = true — When true, Gate 1 auto-selects the top-ranked idea (highest pilot signal + novelty confirmed) and continues to implementation. When false, always waits for explicit user confirmation before proceeding.
• ARXIV_DOWNLOAD = false — When true, /research-lit downloads the top relevant arXiv PDFs during literature survey. When false (default), only fetches metadata via arXiv API. Passed through to /idea-discovery → /research-lit.
• HUMAN_CHECKPOINT = false — When true, the auto-review loops (Stage 3) pause after each round's review to let you see the score and provide custom modification instructions before fixes are implemented. When false (default), loops run fully autonomously. Passed through to /auto-review-loop.
• REVIEWER_DIFFICULTY = medium — How adversarial the reviewer is. medium (default): standard MCP review. hard: adds reviewer memory + debate protocol. nightmare: GPT reads repo directly via codex exec + memory + debate. Passed through to /auto-review-loop.
• CODE_REVIEW = true — GPT-5.5 xhigh reviews experiment code before deployment. Catches logic bugs before wasting GPU hours. Set false to skip. Passed through to /experiment-bridge.
• BASE_REPO = false — GitHub repo URL to use as base codebase. When set, /experiment-bridge clones the repo first and implements experiments on top of it. When false (default), writes code from scratch or reuses existing project files. Passed through to /experiment-bridge.
• COMPACT = false — When true, generates compact summary files for short-context models and session recovery. Passed through to /idea-discovery and /experiment-bridge.
• AUTO_WRITE = false — When true, automatically invoke Workflow 3 (/paper-writing) after Stage 4. Requires VENUE to be set. When false (default), Stage 4 generates NARRATIVE_REPORT.md and stops — user invokes /paper-writing manually.
• VENUE = ICLR — Target venue for paper writing (Stage 5). Only used when AUTO_WRITE=true. Options: ICLR, NeurIPS, ICML, CVPR, ACL, AAAI, ACM, IEEE_CONF, IEEE_JOURNAL.
• RENDER_HTML = true — When true (default), auto-render NARRATIVE_REPORT.md to HTML at Stage 4 completion via /render-html. Uses --no-review (this is an internal handoff doc to /paper-writing, not a reviewer-facing final artifact — the upstream Stage 3 auto-review loop already cross-model-reviewed the claims). Set false to skip, or pass — render html: false. Non-blocking: if /render-html fails or Codex MCP is unavailable, log the failure and continue — the HTML view is a nice-to-have, not a Stage 4 prerequisite.

• RESUMABLE = true — When true (default), the pipeline records per-stage state to .aris/runs/<run_id>.json so a crashed/interrupted run can resume via /research-pipeline — resume <run_id> instead of restarting. Stage status splits done (executor finished writing) from accepted (the stage's cross-model gate / deterministic verifier passed); resume re-validates any done-but-unaccepted stage. See shared-references/resumable-runs.md.

💡 Override via argument, e.g., /research-pipeline "topic" — AUTO_PROCEED: false, human checkpoint: true, difficulty: nightmare, code review: false, base repo: https://github.com/org/project, auto_write: true, venue: NeurIPS.

Overview

This skill chains the entire research lifecycle into a single pipeline:

/idea-discovery → /experiment-bridge → /auto-review-loop → /paper-writing (optional)
├── Workflow 1 ──┤├── Workflow 1.5 ──┤├── Workflow 2 ───┤ ├── Workflow 3 ──┤

It orchestrates up to four major workflows in sequence. Workflow 3 (paper writing) is optional and controlled by AUTO_WRITE.

Resumable runs (— resume <run_id>)

This pipeline is long and can fail mid-run; it tracks per-stage state via run_state.py so you can resume instead of restarting (see [shared-references/resumable-runs.md](shared-references/resumable-runs.md)). Skip this whole section if RESUMABLE = false.

Resolve the helper via the canonical chain (integration-contract §2): .aris/tools/run_state.py → tools/run_state.py → $ARIS_REPO/tools/run_state.py (warn-and-skip if unresolved — never block the pipeline).

Phases, in order: idea-discovery, experiment-bridge, auto-review-loop, summary, paper-writing.

• At start: if — resume <run_id> was passed, run

run_state.py resume <root> <run_id> — it prints the first non-accepted phase; begin the pipeline at that stage (re-run a running/failed stage; re-audit a done-but-unaccepted stage). Otherwise derive <run_id> from the direction slug + date and run_state.py start <root> <run_id> --phases "idea-discovery,experiment-bridge,auto-review-loop,summary,paper-writing".

• Per stage: set <run_id> <phase> running on entry; `set <run_id> <phase>

done --artifact <path>` once the stage's artifact is written.

• Mark accepted ONLY after the stage's gate passes — never on the executor's

own say-so (run_state.py accept requires a recorded verdict id + reviewer):

| phase | what sets accepted | record as reviewer | |-------|----------------------|--------------------| | idea-discovery | Gate 1 cross-model jury / novelty-check passed | codex-gpt-5.5 + thread id | | experiment-bridge | experiments actually ran (jobs completed) — deterministic | deterministic:experiment-bridge | | auto-review-loop | the loop hit its positive STOP (score>=6 AND verdict∈{ready,almost} — codex's verdict) | codex-gpt-5.5 + final review trace id | | summary | NARRATIVE_REPORT.md written (+ rendered if RENDER_HTML) — deterministic | deterministic:summary | | paper-writing | submission audits passed (verify_paper_audits.sh exit 0) — deterministic | deterministic:verify_paper_audits.sh |

If AUTO_WRITE = false (default), paper-writing is not part of this run: after summary is accepted, set <run_id> paper-writing skipped so resume reports COMPLETE instead of pointing forever at a pending stage. Record each accept verdict_id as a durable handle — the codex thread/trace id, or the path/sha of the deterministic verifier's report (e.g. the verify_paper_audits.sh output JSON) — not just the reviewer label.

A stage left done (gate failed/ambiguous, or the run crashed before the gate) is re-validated on the next resume — the acceptance obligation is never skipped.

Pipeline

Stage 1: Idea Discovery (Workflow 1)

If RESEARCH_BRIEF.md exists in the project root, it will be automatically loaded as detailed context (replaces one-line prompt). See templates/RESEARCH_BRIEF_TEMPLATE.md.

Invoke the idea discovery pipeline:

/idea-discovery "$ARGUMENTS"

This internally runs: /research-lit → /idea-creator → /novelty-check → /research-review

Output: idea-stage/IDEA_REPORT.md with ranked, validated, pilot-tested ideas.

🚦 Gate 1 — Human Checkpoint:

After idea-stage/IDEA_REPORT.md is generated, pause and present the top ideas to the user:

📋 Idea Discovery complete. Top ideas:

1. [Idea 1 title] — Pilot: POSITIVE (+X%), Novelty: CONFIRMED
2. [Idea 2 title] — Pilot: WEAK POSITIVE (+Y%),