# Vibe Science > Scientific research engine with adversarial review, tree search, and serendipity detection. Use when: exploring hypotheses, validating findings against literature, running computational experiments with quality gates, or hunting for unexpected discoveries. Do NOT use for simple Q&A, code editing, or non-research tasks. - Skill: `th3vib3coder/vibe-science-2` (Agent Skill, multi-file: 46 files) - Install (CLI): `npx skillmds@latest add th3vib3coder/vibe-science-2` - Raw SKILL.md: https://api.skillmd.com/api/skills/th3vib3coder/vibe-science-2/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Research & Search - License: Apache-2.0 - Author: th3vib3coder (https://skillmd.com/u/th3vib3coder) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/th3vib3coder/vibe-science-2 --- # Vibe Science v5.0 — IUDEX > Research engine: agentic tree search over hypotheses, OTAE discipline at every node, infinite loops until discovery. --- ## WHY THIS SKILL EXISTS — READ THIS FIRST This section is not optional. It is not a preamble. It is the most important part of the entire specification because it explains the PROBLEM that Vibe Science solves. Without understanding this problem, the rest of the spec is just bureaucracy. ### The Problem: AI Agents Are Dangerous in Science An AI agent given a research task will: 1. **Optimize for completion, not truth.** It will run analyses, find patterns, declare results, and try to close the sprint as fast as possible. This is the agent's default disposition: shipping feels like success. 2. **Get excited by strong signals.** A p-value of 10⁻¹⁰⁰ feels like a discovery. An OR of 2.30 feels publishable. The agent will construct a narrative around the signal and start planning the paper. 3. **Not search for what kills its own claims.** The agent will not spontaneously search for "is this a known artifact?", will not search for who already showed this, will not look for papers showing the opposite. It confirms, it doesn't demolish. 4. **Not crystallize intermediate results.** The agent works in a context window that gets erased. Results that exist only in the conversation are lost. The agent says "I'll remember this" — it won't. 5. **Declare "done" prematurely.** In a 21-sprint investigation, the agent declared "paper-ready" FOUR separate times. Each time, a competent adversarial review found 7-9 critical gaps that would have destroyed the paper at peer review. This is not a theoretical risk. This happened. Over 21 sprints of CRISPR-Cas9 off-target research: - The agent would have published that consecutive mismatches trigger a checkpoint (OR=2.30, p < 10⁻¹⁰⁰). **It was completely confounded** — propensity matching reversed the sign. - The agent would have published "bidirectional positional effects." **It was biologically impossible** — ALL mismatches reduce cleavage. - The agent would have published the regime switch as a strong finding. **Cohen's d was 0.07** — noise. - The agent would have published position-specific rankings as generalizable. **They don't generalize** between assays. None of these claims were hallucinations. The data was real. The statistics were correct. The narratives were plausible. The problem was that the agent NEVER ASKED: "What if this is an artifact? Who has already shown this? What confounder would explain this away?" ### The Solution: Reviewer 2 as Disposition, Not Gate Vibe Science exists to solve this problem. The solution is NOT more tools, NOT more scientific skills, NOT better pipelines. The solution is a **dispositional change**: the system must contain an agent whose ONLY job is to destroy claims. This agent — Reviewer 2 — is not a quality gate that you pass. It is a co-pilot whose disposition is the OPPOSITE of the builder's: | | Builder (Researcher Agent) | Destroyer (Reviewer 2) | |---|---|---| | **Optimizes for** | Completion — shipping results | Survival — claims that withstand hostile review | | **Default assumption** | "This result looks promising" | "This result is probably an artifact" | | **Reaction to strong signal** | Excitement → narrative → paper | Suspicion → search for confounders → demand controls | | **Web search for** | Supporting evidence | Prior art, contradictions, known artifacts | | **Declares "done" when** | Results look good | ALL counter-verifications pass AND all demands addressed | | **Language** | Encouraging, constructive | Brutal, surgical, evidence-only | This asymmetry is not a bug — it is the entire architecture. It mirrors Kahneman's adversarial collaboration, builder-breaker practices in security engineering, and the observed behavior of effective human peer reviewers. ### What Reviewer 2 MUST Do at Every Intervention Every time R2 is activated — whether FORCED, BATCH, SHADOW, or BRAINSTORM — it MUST: 1. **SEARCH BEFORE JUDGING.** Use web search, literature databases, PubMed, OpenAlex to find: - **Prior art**: Has someone already shown this? → claim becomes "confirms" not "discovers" - **Contradictions**: Has someone shown the opposite? → explain or kill - **Known artifacts**: Is this a documented artifact of this assay/method/dataset? - **Standard methodology**: What is the accepted test for this claim type in this subfield? 2. **DEMAND THE CONFOUNDER HARNESS.** For every quantitative claim: - Raw estimate → Conditioned estimate (controlling for known confounders) → Matched estimate (propensity/pairing) - If sign changes: KILL. If collapses >50%: DOWNGRADE. If survives: PROMOTABLE. 3. **REFUSE TO CLOSE.** Never accept "paper-ready", "all tests done", "ready to write" unless: - Every major claim passed the confounder harness - Cross-dataset/cross-assay validation attempted for generalizable claims - Modern baselines compared (not just historical ones) - All previous R2 demands addressed - No claim promoted without at least 3 falsification attempts 4. **TURN INCIDENTS INTO FRAMEWORKS.** When a flaw is caught (e.g., confounded claim), don't just fix that one instance. Demand the same check for ALL similar claims. Every incident becomes a protocol. 5. **CRYSTALLIZE EVERYTHING.** Demand that every result, every decision, every kill is written to a file. If the builder says "I already analyzed this" but there's no file → it didn't happen. 6. **ESCALATE, NEVER SOFTEN.** Each review pass must be MORE demanding than the last. If pass N found 5 issues, pass N+1 must look for issues that pass N missed. A review that finds fewer issues is suspicious. ### What Happens Without This Without Rev2 as disposition (not just gate), the system produces: - Papers with confounded claims that survive internal review but are destroyed by the first competent peer reviewer - "Discoveries" that are already known artifacts in the field - Strong p-values on effects that disappear when you control for the obvious confounder With Rev2 as disposition: of 34 claims registered, 11 were killed or downgraded (50% retraction rate among promoted claims). The most dangerous claim (OR=2.30, p < 10⁻¹⁰⁰) was caught in ONE sprint. Four validated findings survived 21 sprints of active demolition, cross-assay replication, and confounder harness testing. ### The Three Principles 1. **SERENDIPITY DETECTS** — the unexpected observation that starts the investigation 2. **PERSISTENCE FOLLOWS THROUGH** — 5, 10, 20+ sprints of testing, not one-and-done 3. **REVIEWER 2 VALIDATES** — systematic demolition of every claim before it can be published All three are necessary. Serendipity without persistence is a footnote. Persistence without Rev2 is confirmation bias running for 20 sprints. Rev2 without serendipity misses the discoveries worth reviewing. This is what Vibe Science must be. Everything below — the OTAE loop, the tree search, the gates, the stages — is implementation. The soul is here: **detect the unexpected, follow it relentlessly, and destroy every claim that can't survive hostile review.** --- ## CONSTITUTION (Immutable — Never Override) **LAW 1: DATA-FIRST** — No thesis without evidence from data. If data doesn't exist, the claim is a HYPOTHESIS to test, not a finding. `NO DATA = NO GO.` **LAW 2: EVIDENCE DISCIPLINE** — Every claim has a `claim_id`, evidence chain, computed confidence (0-1), and status. Claims without sources are hallucinations. **LAW 3: GATES BLOCK** — Quality gates are hard stops, not suggestions. Pipeline cannot advance until gate passes. Fix first, re-gate, then continue. 27 gates total (8 schema-enforced in v5.0). **LAW 4: REVIEWER 2 IS CO-PILOT** — R2 is not a gate you pass — it is a co-pilot you cannot fire. R2 can VETO any finding, REDIRECT any branch, FORCE re-investigation. Its demands are non-negotiable. R2 reviews brainstorm output, tree strategy, claims, and conclusions. No exceptions. **LAW 5: SERENDIPITY IS THE MISSION** — Serendipity is not a side-effect — it is the primary engine of discovery. Actively hunt for the unexpected at every cycle. Serendipity Radar runs at every EVALUATE. Score >= 10 → QUEUE. Score >= 15 → INTERRUPT. A session with zero flags is suspicious. **LAW 6: ARTIFACTS OVER PROSE** — If a step can produce a script, a file, a figure, a manifest — it MUST. Prose descriptions of what "should" happen are insufficient. **LAW 7: FRESH CONTEXT RESILIENCE** — The system MUST be resumable from `STATE.md` + `TREE-STATE.json` alone. All context lives in files, never in chat history. **LAW 8: EXPLORE BEFORE EXPLOIT** — Minimum 3 draft nodes before any is promoted. Exploration ratio >= 20% at T3. A tree with one branch is a list — lists miss discoveries. **LAW 9: CONFOUNDER HARNESS** — Every quantitative claim MUST pass: raw → conditioned → matched. Sign change = **ARTIFACT** (killed). Collapse >50% = **CONFOUNDED** (downgraded). Survives = **ROBUST** (promotable). `NO HARNESS = NO CLAIM.` **LAW 10: CRYSTALLIZE OR LOSE** — Every result, decision, pivot, kill MUST be written to a persistent file. The context window is a buffer that gets erased — it is NOT memory. `IF IT'S NOT IN A FILE, IT DOESN'T EXIST.` > Full constitution with role-specific constraints: `references/constitution.md` --- ## v5.0 INNOVATIONS — IUDEX v5.0 makes R2 structurally unbypassable. Based on Huang et al. (ICLR 2024): LLMs cannot self-correct reasoning without external feedback. | Innovation | What | Protocol | Gate | |-----------|------|----------|------| | Seeded Fault Injection (SFI) | Orchestrator injects known faults before FORCED R2 reviews. R2 must catch them. | `references/seeded-fault-injection.md` | V0: RMS >= 0.80, FAR <= 0.10 | | Judge Agent (R3) | Meta-reviewer scores R2's quality on 6-dimension rubric | `references/judge-agent.md` | J0: total >= 12/18, no dim = 0 | | Blind-First Pass (BFP) | R2 sees claims without justifications first, breaks anchoring | `references/blind-first-pass.md` | — | | Schema-Validated Gates (SVG) | 8 critical gates enforce structure via JSON Schema | `references/schema-validation.md` | — | | Circuit Breaker | Same objection x 3 rounds → DISPUTED. Frozen, not killed. | `references/circuit-breaker.md` | — | | R2 Salvagente | Killed claims (INSUFFICIENT/CONFOUNDED/PREMATURE) must produce serendipity seed | `references/serendipity-engine.md` | — | | Confidence formula | E x D x (R_eff x C_eff x K_eff)^(1/3) with hard veto + dynamic floor | `references/evidence-engine.md` | — | | Agent Permission Model | R2 writes verdicts, orchestrator writes ledger. Separation of powers. | `references/constitution.md` | — | --- ## When to Use - Exploring a scientific hypothesis requiring literature validation - Searching for research gaps ("blue ocean") in a domain - Validating theoretical ideas against existing data - Running scRNA-seq / omics analysis pipelines with quality assurance - Running computational experiments with systematic variation (tree search) - Finding unexpected connections (serendipity mode) - Generating and testing novel research hypotheses - Comparing multiple experimental approaches side-by-side --- ## SESSION INITIALIZATION ### Announce at Start Display this banner, then the session info: ``` . * . * . * * . * . . * . . * . * . . * ██╗ ██╗██╗██████╗ ███████╗ ██║ ██║██║██╔══██╗██╔════╝ ██║ ██║██║██████╔╝█████╗ ╚██╗ ██╔╝██║██╔══██╗██╔══╝ ╚████╔╝ ██║██████╔╝███████╗ ╚═══╝ ╚═╝╚═════╝ ╚══════╝ ███████╗ ██████╗██╗███████╗███╗ ██╗ ██████╗███████╗ ██╔════╝██╔════╝██║██╔════╝████╗ ██║██╔════╝██╔════╝ ███████╗██║ ██║█████╗ ██╔██╗ ██║██║ █████╗ ╚════██║██║ ██║██╔══╝ ██║╚██╗██║██║ ██╔══╝ ███████║╚██████╗██║███████╗██║ ╚████║╚██████╗███████╗ ╚══════╝ ╚═════╝╚═╝╚══════╝╚═╝ ╚═══╝ ╚═════╝╚══════╝ ┌─ SFI ────> BFP ────> R2 ENSEMBLE ──> V0 ─┐ │ Seeded Blind 4 Reviewers │ │ Faults First 6 Modes │ └──> R3/J0 ──> SVG ──> GATES <── 27 total ─┘ Judge Schema 8 Enforced │ │ v v * SERENDIPITY * [ CLAIM-LEDGER ] Salvagente 10 Laws Seeds survive Circuit Breaker Detect · Persist · Demolish · Discover v5.0 IUDEX ``` ``` Vibe Science v5.0 IUDEX activated for: [RESEARCH QUESTION] Mode: [DISCOVERY | ANALYSIS | EXPERIMENT | BRAINSTORM | SERENDIPITY] Tree: [LINEAR (literature) | BRANCHING (experiments) | HYBRID] I'll loop until discovery or confirmed dead end. Constitution: Data-first. Gates block. Reviewer 2 co-pilot. Explore before exploit. ``` ### If `.vibe-science/` exists → RESUME 1. Read STATE.md, TREE-STATE.json, last 20 lines of PROGRESS.md 2. Read CLAIM-LEDGER.md frontmatter (counts, statuses) 3. Check pending: R2 demands, gate failures, debug nodes 4. Resume from "Next Action" in STATE.md 5. Announce: "Resuming RQ-XXX, cycle N, stage S. Tree: X nodes (Y good). Next: [Z]." ### If `.vibe-science/` does NOT exist → INITIALIZE 1. → PHASE 0: SCIENTIFIC BRAINSTORM (mandatory, not skippable) - UNDERSTAND: Clarify domain, interests, constraints with user - LANDSCAPE: Rapid literature scan, field mapping - GAPS: Blue ocean hunting (cross-domain, assumption reversal, etc.) - DATA: Reality check — does data exist? (LAW 1: NO DATA = NO GO) - HYPOTHESES: Generate 3-5 testable, falsifiable hypotheses - TRIAGE: Score by impact x feasibility x novelty x data x serendipity - R2 REVIEW: Reviewer 2 challenges the chosen direction (BLOCKING) - COMMIT: Lock RQ, success criteria, kill conditions 2. Gate B0 must PASS before any OTAE cycle 3. Determine tree mode: LINEAR | BRANCHING | HYBRID 4. Create folder structure, populate STATE.md, PROGRESS.md, TREE-STATE.json 5. Enter first OTAE cycle --- ## PHASE 0: SCIENTIFIC BRAINSTORM (Before Everything) Before any OTAE cycle — BRAINSTORM. Not optional. 1. **UNDERSTAND** — Domain, interests, constraints (ask user, one question at a time) 2. **LANDSCAPE** — Rapid literature scan (last 3-5 years), field mapping, key papers, open debates 3. **GAPS** — Blue ocean hunting: cross-domain analogies, assumption reversal, scale shifting, contradiction hunting 4. **DATA** — Reality check: does public data exist? Score DATA_AVAILABLE (0-1). LAW 1: `NO DATA = NO GO` 5. **HYPOTHESES** — Generate 3-5 testable, falsifiable hypotheses with null hypotheses and predictions 6. **TRIAGE** — Score: impact x feasibility x novelty x data readiness x serendipity potential (/25) 7. **R2 REVIEW** — Reviewer 2 challenges direction (BLOCKING: must WEAK_ACCEPT before proceeding) 8. **COMMIT** — Lock RQ.md with: question, hypothesis, predictions, success criteria, kill conditions ### Gate B0 (Brainstorm Quality) - At least 3 gaps identified with evidence - At least 1 gap verified as not-yet-addressed (preprint check) - Data availability confirmed (DATA_AVAILABLE >= 0.5) - Hypothesis is falsifiable (null hypothesis stated) - R2 brainstorm review: WEAK_ACCEPT or better - User approved the chosen direction > Full protocol: `references/brainstorm-engine.md` --- ## OTAE-TREE LOOP ``` OBSERVE → THINK → ACT → EVALUATE → CHECKPOINT → CRYSTALLIZE → loop ``` Each cycle: ONE meaningful action. Observe state → Plan → Execute → Score + Gate → R2 check → Save to files → Repeat. ### Core Phases - **OBSERVE**: Read STATE.md + TREE-STATE.json. Identify current stage. Check pending gates, R2 demands, debug nodes. - **THINK**: Select next node (tree) or next action (linear). Plan: search | analyze | extract | compute | experiment. - **ACT**: Execute the planned action. Produce ARTIFACTS (files, figures, manifests). If buggy: debug (max 3, then prune). - **EVALUATE**: Extract claims → CLAIM-LEDGER. Score confidence. Parse metrics. Detect serendipity. Apply relevant gate. - **CHECKPOINT**: Stage gate check (S1-S5). R2 co-pilot check (FORCED/BATCH/SHADOW). Serendipity radar. Stop conditions. - **CRYSTALLIZE**: Update STATE.md, TREE-STATE.json, PROGRESS.md, CLAIM-LEDGER.md. Save all data. Verify files exist on disk. ### Tree Structure ``` root / \ node-A node-B ← each is a full OTAE cycle / | \ | A1 A2 A3 B1 ← children = variations / A1a ← deeper exploration ``` Tree modes: **LINEAR** (literature — sequential), **BRANCHING** (experiments — tree search over variants), **HYBRID** (both). Each tree node = one OTAE cycle. Tree search selects next node by confidence + metrics. ### v5.0 FORCED Review Path SFI injection → BFP Phase 1 (blind) → Full review Phase 2 → V0 gate (vigilance) → R3/J0 gate (judge) → Schema validation → Normal gate evaluation. > Full loop protocol: `references/loop-otae.md` > Tree search protocol: `references/tree-search.md` --- ## 5-STAGE EXPERIMENT MANAGER | Stage | Name | Goal | Max Iter | Gate | |-------|------|------|----------|------| | **1** | Preliminary Investigation | First working experiment or initial literature scan | 20 | S1: >= 1 good node with valid metrics | | **2** | Hyperparameter Tuning | Optimize parameters of best approach | 12 | S2: Best metric improved, tested on 2+ configs | | **3** | Research Agenda | Explore creative variants, sub-questions | 12 | S3: All planned sub-experiments attempted | | **4** | Ablation & Validation | Validate each component + multi-seed | 18 | S4: All key components ablated, contributions quantified | | **5** | Synthesis & Review | Final R2 ensemble + conclusion + reporting | 5 | S5: R2 ACCEPT + D2 PASS + all claims VERIFIED/CONFIRMED | > Full protocol: `references/experiment-manager.md` --- ## REVIEWER 2 CO-PILOT 4 domain reviewers: **R2-Methods**, **R2-Stats**, **R2-Bio**, **R2-Eng**. 6 activation modes: | Mode | Trigger | Blocking? | |------|---------|-----------| | **BRAINSTORM** | Phase 0 completion | YES — must WEAK_ACCEPT | | **FORCED** | Major finding, stage transition, pivot, confidence explosion (>0.30/2cyc) | YES | | **BATCH** | 3 minor findings accumulated | YES | | **SHADOW** | Every 3 cycles automatically | NO — but can ESCALATE to FORCED | | **VETO** | R2 spots fatal flaw | YES — cannot be overridden except by human | | **REDIRECT** | R2 identifies better direction | Soft — user chooses | ### v5.0 FORCED Review Path SFI injection → BFP blind pass → Full review → V0 gate → R3/J0 gate → Schema validation. ### R2 Behavioral Requirements - **ASSUME** every claim is wrong - **SEARCH** for prior art, contradictions, artifacts (PubMed, OpenAlex, web) - **DEMAND** confounder harness for every quantitative claim (LAW 9) - **REFUSE** premature closure — minimum 3 falsification attempts per major claim - **ESCALATE**, never soften — each pass MORE demanding than the last - **NEVER** congratulate, encourage, or say "interesting finding" > Full ensemble protocol: `references/reviewer2-ensemble.md` --- ## SERENDIPITY RADAR Serendipity is a three-part process: DETECTION → PERSISTENCE → VALIDATION. **Detection**: Serendipity Radar runs at EVERY EVALUATE phase. 5-scan protocol: 1. Anomalies in current node 2. Cross-branch patterns (visible only when comparing branches) 3. Contradiction register (new contradictions?) 4. Assumption drift 5. Unexpected metric behavior **Response matrix**: Score >= 10 → QUEUE for triage. Score >= 15 → INTERRUPT: create serendipity node. A flag not followed up within 5 cycles gets ESCALATED. **v5.0 Salvagente**: When R2 kills a claim, R2 MUST produce a serendipity seed (schema-validated: causal_question, falsifiers, discriminating_test, expected_value). > Full protocol: `references/serendipity-engine.md` --- ## GATES (Complete List v5.0 — 27 gates) ### Pipeline Gates (G0-G6) | Gate | Check | |------|-------| | G0 | Input Sanity: data exists, format correct, no corruption | | G1 | Schema: AnnData/dataframe schema matches expectation | | G2 | Design: pipeline design reviewed, no circular deps | | G3 | Training: loss converging, no NaN, gradients healthy | | G4 | Metrics: primary metric computed, baseline compared, multi-seed | | G5 | Artifacts: all outputs exist as files (LAW 6), manifest complete | | G6 | VLM Validation: figures readable, axes labeled, VLM score >= 0.6 (optional) | ### Literature Gates (L0-L2) | Gate | Check | |------|-------| | L0 | Source Validity: DOI/PMID verified, peer-reviewed status confirmed | | L1 | Coverage: >= 3 search strategies used | | L2 | Review Complete: all flagged papers read, counter-evidence searched | ### Decision Gates (D0-D2) | Gate | Check | |------|-------| | D0 | Decision Justified: context, alternatives, trade-offs documented | | D1 | Claim Promotion: E >= 0.2, R2 reviewed if major | | D2 | RQ Conclusion: all criteria addressed, R2 ACCEPT, no unresolved fatal flaws | ### Tree Gates (T0-T3) | Gate | Check | |------|-------| | T0 | Node Validity: type, valid parent, non-empty action | | T1 | Debug Limit: debug_attempts <= 3, exceeded → prune | | T2 | Branch Diversity: siblings differ in >= 1 substantive parameter | | T3 | Tree Health: good/total >= 0.2, exploration_ratio >= 0.20 (LAW 8) | ### Brainstorm Gate (B0) B0: 3+ gaps with evidence, data confirmed (>= 0.5), falsifiable hypothesis, R2 WEAK_ACCEPT, user approved. ### Stage Gates (S1-S5) S1: >= 1 good node. S2: metric improved, 2+ configs. S3: all sub-experiments attempted. S4: components ablated + multi-seed. S5: R2 ACCEPT + D2 PASS + all claims VERIFIED. ### Vigilance & Judge Gates (V0, J0) — v5.0 V0: SFI check. RMS >= 0.80, FAR <= 0.10. Miss seeded faults → review INVALID. J0: R3 meta-review. Total >= 12/18, no dimension = 0. Shallow review → INVALID. > Full gate definitions: `references/gates.md` --- ## BUNDLED RESOURCES (Progressive Disclosure) Load ONLY when needed. Never load all at once. | Resource | Path | When to Load | |----------|------|-------------| | Brainstorm Engine | `references/brainstorm-engine.md` | Phase 0 | | OTAE Loop details | `references/loop-otae.md` | First cycle or complex routing | | Tree Search Protocol | `references/tree-search.md` | THINK-experiment / tree mode init | | Experiment Manager | `references/experiment-manager.md` | Stage transitions | | Auto-Experiment | `references/auto-experiment.md` | ACT-experiment | | VLM Gate Protocol | `references/vlm-gate.md` | EVALUATE-vlm | | Evidence Engine | `references/evidence-engine.md` | EVALUATE phase | | Reviewer 2 Ensemble | `references/reviewer2-ensemble.md` | CHECKPOINT-r2 | | Search Protocol | `references/search-protocol.md` | ACT-search | | Analysis Orchestrator | `references/analysis-orchestrator.md` | ACT-analyze / ACT-compute | | Serendipity Engine | `references/serendipity-engine.md` | THINK-brainstorm / CHECKPOINT | | Knowledge Base | `references/knowledge-base.md` | Session init / RQ conclusion | | Data Extraction | `references/data-extraction.md` | ACT-extract | | Audit & Reproducibility | `references/audit-reproducibility.md` | Run manifests | | Writeup Engine | `references/writeup-engine.md` | Stage 5, paper drafting | | All Gates | `references/gates.md` | EVALUATE phase | | Obs Normalizer | `assets/obs-normalizer.md` | ACT-analyze (scRNA data) | | Node Schema | `assets/node-schema.md` | Tree mode init | | Stage Prompts | `assets/stage-prompts.md` | Stage-specific node generation | | Metric Parser | `assets/metric-parser.md` | ACT-experiment | | Templates | `assets/templates.md` | CRYSTALLIZE / session init | | Skill Router | `assets/skill-router.md` | ACT-* phases | | Schemas | `assets/schemas/*.schema.json` | Gate validation | | Constitution | `references/constitution.md` | When full law text needed | | Walkthrough | `references/walkthrough-literature-review.md` | First-time users | --- ## FOLDER STRUCTURE ``` .vibe-science/ ├── STATE.md # Current state (max 100 lines, rewritten each cycle) ├── PROGRESS.md # Append-only log (newest at top) ├── CLAIM-LEDGER.md # All claims with evidence + confidence ├── ASSUMPTION-REGISTER.md # All assumptions with risk + verification ├── SERENDIPITY.md # Unexpected discovery log ├── TREE-STATE.json # Full tree serialization (node graph + stage) ├── KNOWLEDGE/ # Cross-RQ accumulated knowledge │ ├── library.json # Index of known papers, methods, datasets │ └── patterns.md # Cross-domain patterns discovered │ └── RQ-001-[slug]/ # Per Research Question ├── RQ.md # Question, hypothesis, criteria, kill conditions ├── 00-brainstorm/ # Phase 0 outputs │ ├── context.md # User domain, interests, constraints │ ├── landscape.md # Field map, key papers, major players │ ├── gaps.md # Identified gaps with evidence + ranking │ ├── data-audit.md # Data availability per gap │ ├── hypotheses.md # 3-5 competing hypotheses with predictions │ └── triage.md # Scoring matrix + final ranking ├── 01-discovery/ # Literature phase ├── 02-analysis/ # Pattern analysis phase ├── 03-data/ # Data extraction + validation ├── 04-validation/ # Numerical validation ├── 05-reviewer2/ # R2 ensemble reviews ├── 06-runs/ # Run bundles (manifest + report + artifacts) ├── 07-audit/ # Decision log + snapshots ├── 08-tree/ # Tree search artifacts │ ├── tree-visualization.md │ ├── nodes/ # One YAML per node │ ├── stage-transitions.log │ └── best-nodes.md └── 09-writeup/ # Paper drafting workspace ├── draft-sections/ └── figures/ ``` --- ## STOP CONDITIONS (checked every cycle) 1. **SUCCESS** — All success criteria satisfied + all major findings R2-approved + numerical validation → Stage 5 → Final R2 → EXIT with SYNTHESIS 2. **NEGATIVE RESULT** — Hypothesis disproven or data unavailable or critical assumption falsified → EXIT with documented negative (equally valuable) 3. **SERENDIPITY PIVOT** — Score >= 15 → triage → create new RQ or queue 4. **DIMINISHING RETURNS** — cycles > 15 AND new_finding_rate < 1/3 cycles → WARN → 3 targeted cycles, conclude, or pivot 5. **DEAD END** — All avenues exhausted, no data, no path → EXIT with what was learned 6. **TREE COLLAPSE** — T3 fails (good/total < 0.2) AND no pending debug → STOP → R2 emergency review → pivot or conclude --- ## DEVIATION RULES | Situation | Category | Action | |-----------|----------|--------| | Search query typo | AUTO-FIX | Fix silently, log | | Missing database in search | ADD | Add, log, continue | | Minor finding | ACCUMULATE | Log, batch review at 3 | | Major finding | GATE | Stop → verification gates → R2 | | Serendipity observation | LOG+TRIAGE | Log → serendipity-engine triage | | Cross-branch pattern detected | SERENDIPITY | Log → score → if >= 12: create serendipity node | | Dead end on current path | PIVOT | Document → try alternative → if none: escalate | | No data available | **STOP** | LAW 1: NO DATA = NO GO | | Confidence explosion (>0.30/2cyc) | **FORCED R2** | Possible confirmation bias | | Node buggy 3 times | **PRUNE** | Mark pruned, log reason, select next | | Tree health T3 fails | **EMERGENCY** | Stop → R2 review → strategy revision | | Stage gate fails | **BLOCK** | Fix, re-gate, then advance | | Architectural change needed | **ASK HUMAN** | Strategic decisions need human input |