Method Framework Design

Update the literature record: Any new papers found during Phase 3 should be added to docs/02_literature/paper-list.md with a note: [Found during Phase 3 — method design].

If search fails (no results, paywall, or tools unavailable): do NOT fabricate an answer. Instead:

1. Note the specific question that needs answering: "Need to know: [question]"
2. Record it in the exploration report
3. Ask the user: "I couldn't find information on [X]. Do you know, or can you check?"
4. Continue with what you know, marking the gap as an assumption to verify

This applies equally to Phase 4, 5, and 6. Literature retrieval is a continuous activity, not a one-time Phase 1 task. </IRON-LAW>

Re-Entry from Phase 4a (Exploratory Return Path)

If the user returns to Phase 3 from Phase 4a exploration (because baseline results or data analysis revealed the method/analysis design needs rethinking), do NOT start from scratch:

1. Read the Phase 4a exploration report (docs/05_execution/phase4a-exploration-report.md)
2. Carry forward what was learned:
   • Type M: baseline performance, actual failure patterns (may differ from predicted), error analysis
   • Type D: data characteristics, patterns found in EDA, what analyses are/aren't promising
3. Targeted redesign: Only redesign the parts that the exploration revealed as problematic. If the evaluation protocol is still valid, keep it. If the innovation point needs adjustment, adjust only that.
4. Re-run the multi-agent design deliberation (M-Step 5 or D-Step 4) with the new context — agents should have access to the Phase 4a exploration report
5. Update G2 outputs — the revised plan goes through G2 checklist again before re-entering Phase 4b

Branching Logic

digraph branching {
    rankdir=TB;
    start [label="G1 passed\nresearch-anchor.yaml confirmed" shape=doublecircle];
    check [label="research_type?" shape=diamond];
    M [label="Type M Path\n(Method Development)" shape=box style=filled fillcolor="#d4edda"];
    D [label="Type D Path\n(Discovery / Data Analysis)" shape=box style=filled fillcolor="#cce5ff"];
    C [label="Type C Path\n(Tool / Software)" shape=box style=filled fillcolor="#e0d4ff"];
    H [label="Type H Path\nExecute BOTH tracks\nMark primary track" shape=box style=filled fillcolor="#fff3cd"];
    gate [label="G2 Gate\nPlan Freeze Checklist" shape=doubleoctagon style=filled fillcolor="#f8d7da"];

    start -> check;
    check -> M [label="M"];
    check -> D [label="D"];
    check -> C [label="C"];
    check -> H [label="H"];
    M -> gate;
    D -> gate;
    C -> gate;
    H -> gate;
}

Read research_type from docs/01_intake/research-anchor.yaml. If absent, STOP and invoke domain-anchoring first.

Type M Path — Method Development

M-Step 1: Lock Evaluation Protocol

REQUIRED SUB-SKILL: Invoke amplify:evaluation-protocol-design if available. If unavailable, follow the procedure below.

For each item, propose with justification, then get explicit user confirmation before proceeding:

1. Primary metrics — why these measure the core claim
2. Evaluation protocol — K-fold, train/val/test, episode-based, etc.
3. Seeds — recommend: [42, 123, 456, 789, 1024]
4. Statistical reporting — mean ± std, 95% CI, significance test
5. Evaluation datasets — rationale for each dataset choice

Write to docs/03_plan/evaluation-protocol.yaml using templates/evaluation-protocol.yaml. Set locked: true only after user confirms every item.

M-Step 2: Design Innovation Method

Build on literature insights and cross-domain inspiration from Phase 1–2.

• Innovation Point (limit 1–2): state precisely what is novel
• Value Proposition: why this works — ground in theory or strong intuition
• Predicted failure modes: what could go wrong, and backup plan for each

Write innovation_point and value_proposition to research-anchor.yaml.

M-Step 3: Confirm Baselines and Pre-Existing Results

3a. Consolidate baseline list:

1. Import user_specified baselines from Phase 1 (docs/02_literature/baseline-collection.md) → these are automatically must_include
2. System recommends additional baselines from literature review (target total: 3–5 for must_include)
3. Ask user again: "Are there additional methods you want to compare against?"
4. For each baseline, record:
   • Name and citation
   • Source: official_repo / our_implementation / paper_reported
   • Official code URL (if available)
   • Configuration notes (hyperparameters, training setup)

3b. Check for pre-existing results:

Ask: "Do you already have results for any of these baselines? (e.g., from your own prior experiments, or from a standardized benchmark leaderboard)"

If user provides pre-computed results, for each one verify:

• Which dataset(s) and split(s) were used?
• Which metrics were reported?
• How many seeds/runs? What were the seed values?
• What execution environment? (hardware, software versions)
• Source: user_own_run / paper_reported / leaderboard

Record in evaluation-protocol.yaml baselines section with a pre_computed field.

Compatibility check — once evaluation-protocol.yaml is drafted (M-Step 1), compare pre-computed results against the locked protocol:

Mark each pre-computed result as:

• accepted — fully compatible, no re-run needed
• reference_only — useful context but must re-run for official comparison
• incompatible — must re-run

Write to evaluation-protocol.yaml baselines section.

M-Step 4: Pre-Design Ablation Experiments

For each key component of the proposed method:

M-Step 4b: Theoretical Analysis Plan (Optional but Recommended)

If the proposed method makes claims that can be theoretically grounded, plan the theory work here. This is OPTIONAL — not all method papers need theory. But if the target venue values theoretical justification, this significantly strengthens the paper.

When to include theoretical analysis:

• The method involves a new optimization objective → prove convergence
• The method involves a new algorithm → analyze time/space complexity
• The method makes approximation claims → prove bounds
• The method has correctness requirements → prove correctness
• The target venue is theory-friendly (e.g., NeurIPS, ICML, JMLR, SIAM)

When NOT needed:

• Pure empirical papers at applied venues (e.g., application workshops, domain-specific conferences)
• System/tool papers where the contribution is engineering, not algorithmic
• The method is a straightforward application of existing, already-proven components

If included, plan:

1. What to prove: List specific theorems/propositions (e.g., "Theorem 1: Algorithm converges at rate O(1/√T)")
2. Proof strategy sketch: What mathematical tools will you use? (e.g., Lyapunov analysis, VC theory, concentration inequalities)
3. Required assumptions: What conditions must hold? Are they realistic?
4. Fallback: If the proof doesn't work, what weaker result would still be valuable?

Record in docs/03_plan/theoretical-analysis-plan.md.

M-Step 5: Multi-Agent Method Design Deliberation (AUTOMATED — MANDATORY)

This is ESPECIALLY critical for Type M. Method development research lives or dies by whether the idea is both novel AND effective. </IRON-LAW>

REQUIRED SUB-SKILL: Follow amplify:multi-round-deliberation protocol (max 5 rounds).

Agent composition for Type M:

Dispatch — Round 1 (parallel):

Prepare the context package:

• Research question (from Phase 2)
• Proposed method design (from M-Steps 1-4)
• Innovation point and value proposition
• Baseline list and pre-existing results
• Ablation plan
• Literature review and gap analysis

Agent 1 — Innovation Advisor:

Call Task tool with:
  description: "Innovation Advisor — evaluate method novelty"
  prompt: |
    SHARED VALUES:
    Target venue: [venue]. Research type: Type M.
    Optimization target: "Is this method genuinely novel and impactful?"
    Scoring: PASS / CONDITIONAL / FAIL
    
    You are a senior researcher known for creative, cross-disciplinary 
    thinking. You have a track record of identifying breakthrough ideas 
    and a nose for "just engineering" vs. "true innovation."
    
    PROPOSED METHOD: [paste method design]
    INNOVATION POINT: [paste]
    VALUE PROPOSITION: [paste]
    LITERATURE CONTEXT: [paste key related work]
    
    Evaluate:
    1. NOVELTY: Is the innovation point genuinely new, or a 
       straightforward combination of existing ideas? Be honest.
    2. CROSS-DOMAIN INSPIRATION: Are there ideas from other fields 
       (e.g., NLP for CV, physics for ML, biology for algorithms) 
       that could strengthen or replace this approach?
    3. SIMPLICITY TEST: Is the method more complex than it needs to 
       be? Could a simpler design achieve the same goal?
    4. IMPACT POTENTIAL: If this works perfectly, how much does it 
       move the field forward? Incremental improvement or paradigm shift?
    5. SUGGESTED IMPROVEMENTS: Propose 2-3 ways to make the method 
       more novel, more elegant, or more impactful.
    6. ADDITIONAL LITERATURE NEEDED: Are there papers or techniques 
       that should be reviewed before finalizing? List specific queries.
    7. VERDICT: PASS / CONDITIONAL / FAIL
  subagent_type: "generalPurpose"

Agent 2 — Technical Architect:

Call Task tool with:
  description: "Technical Architect — evaluate method feasibility"
  prompt: |
    SHARED VALUES:
    Target venue: [venue]. Research type: Type M.
    Optimization target: "Can this be built, trained, and evaluated rigorously?"
    Scoring: PASS / CONDITIONAL / FAIL
    
    You are a senior ML/systems engineer who has implemented dozens 
    of research prototypes. You know the difference between a method 
    that looks good on paper and one that actually works in practice.
    
    PROPOSED METHOD: [paste method design]
    EVALUATION PROTOCOL: [paste]
    AVAILABLE RESOURCES: [paste compute, data, timeline]
    
    Evaluate:
    1. IMPLEMENTABILITY: Can this be coded cleanly? Are there 
       ambiguous design choices that will cause problems?
    2. TRAINING/EXECUTION: Are there likely stability issues, 
       convergence problems, or scalability bottlenecks?
    3. EVALUATION RIGOR: Is the evaluation protocol sufficient? 
       Are there missing experiments that reviewers will demand?
    4. RESOURCE FIT: Can this be completed with available resources?
    5. FAILURE MODE ANALYSIS: What are the top 3 ways this method 
       could fail? For each, is there a mitigation plan?
    6. SUGGESTED IMPROVEMENTS: How to make the design more robust, 
       more efficient, or easier to ablate?
    7. VERDICT: PASS / CONDITIONAL / FAIL
  subagent_type: "generalPurpose"

Agent 3 — Baseline Devil's Advocate:

Call Task tool with:
  description: "Baseline Devil's Advocate — challenge method necessity"
  prompt: |
    SHARED VALUES:
    Target venue: [venue]. Research type: Type M.
    Optimization target: "Is this method actually necessary, or can existing methods do the job?"
    Scoring: PASS / CONDITIONAL / FAIL
    
    You are a skeptical reviewer who has seen too many papers claim 
    novelty while ignoring strong baselines. Your job is to ensure 
    the proposed method is genuinely needed and properly compared.
    
    PROPOSED METHOD: [paste method design]
    BASELINE LIST: [paste]
    PRE-COMPUTED RESULTS: [paste if any]
    ABLATION PLAN: [paste]
    
    Evaluate:
    1. BASELINE STRENGTH: Are the baselines strong enough? Are any 
       obvious competitors missing? Would a reviewer say "but you 
       didn't compare with X"?
    2. SIMPLER ALTERNATIVE: Could a simpler method (e.g., a well-tuned 
       existing method, a straightforward ensemble, a basic modification) 
       achieve comparable results? Propose specific alternatives.
    3. ABLATION COMPLETENESS: Does the ablation plan cover all key 
       design choices? Are there components that seem unnecessary?
    4. EXPERIMENT SUFFICIENCY: Are there enough experiments to convince 
       a skeptical reviewer? Suggest additional experiments that would 
       strengthen the paper.
    5. FAIRNESS: Are baselines given fair computational budgets, 
       hyperparameter tuning, and data access?
    6. EXPERIMENT VOLUME: Is the experimental plan SUFFICIENT for 
       the target venue, or does it need more content? Suggest 
       experiments to add (it's better to plan slightly more and 
       filter later than to discover gaps in Phase 5).
    7. VERDICT: PASS / CONDITIONAL / FAIL
  subagent_type: "generalPurpose"

Multi-round deliberation:

After Round 1, follow amplify:multi-round-deliberation:

• Synthesize feedback and refine the method design
• Search for additional literature if any agent flagged knowledge gaps
• Re-dispatch ALL three agents with the complete refined design
• Repeat until all PASS or 5 rounds reached

If Innovation Advisor requests additional literature: Execute a targeted search IMMEDIATELY (web search, arXiv) before the next round. Add findings to the literature record.

Present deliberation results to user:

Method Design Deliberation Results:
════════════════════════════════════

Rounds completed: [N] / max 5

Method design changes through deliberation:
  Round 1 → 2: [what changed]
  Round 2 → 3: [what changed]
  ...

Agent verdicts:
  Innovation Advisor:         [PASS/COND/FAIL] — [summary]
  Technical Architect:        [PASS/COND/FAIL] — [summary]  
  Baseline Devil's Advocate:  [PASS/COND/FAIL] — [summary]

Additional experiments suggested:
  REQUIRED: [list]
  RECOMMENDED: [list]

Additional literature found during deliberation:
  [list new papers if any]

M-Step 6: Confirm Story Line

Present the complete narrative arc (refined by deliberation) for user approval:

Motivation → Insight → Method → Expected Results → Analysis Plan

Do NOT proceed until user explicitly approves.

Type D Path — Discovery / Data Analysis

Type D does NOT need alternative method comparison. Type D is results-driven, not method-driven.

REQUIRED SUB-SKILL: Invoke amplify:analysis-storyboard-design before finalizing the Type D plan. If unavailable, follow the D-Step process below manually.

D-Step 0: Data Choice Validation (BEFORE designing any analysis)

Check 1 — Has this dataset been exhaustively analyzed? Search for papers and tutorials that have analyzed this exact dataset. If the dataset is a standard tutorial/benchmark dataset (e.g., PBMC 3k, Iris, MNIST), it has almost certainly been analyzed with the exact tools you plan to use.

Check 2 — Can standard tools on this data yield NEW findings? If the answer is "probably not" (e.g., everyone already knows what cell types are in PBMC 3k), then either:

• Choose a different, less-studied dataset
• Apply a genuinely novel analytical angle
• Design a comparative study (multiple datasets, conditions, or timepoints)

Check 3 — Does the data have enough complexity for discovery? A single-sample, well-characterized dataset (e.g., one healthy donor's blood) may not contain enough biological variation to support novel findings. Consider: multiple conditions? Disease vs. healthy? Time series? Multiple tissues?

If the data fails any check, present alternatives to the user:

The dataset [name] may not support novel discovery because:
[reason from checks above]

Alternatives that could yield stronger findings:
1. [Suggest a less-studied dataset in the same domain]
2. [Suggest adding a comparative dimension]
3. [Suggest a different analytical angle]

Which direction would you prefer?

D-Step 1: Design Analysis Framework

Plan analysis dimensions in order:

1. Descriptive statistics & data characterization
2. Main analysis (hypothesis testing / modeling)
3. Mechanism exploration (why does the pattern exist?)
4. Robustness checks (sensitivity, subgroups, alternative specs)
5. Exploratory analysis (unexpected patterns)

Define the story structure:

• 1 main story line + 2–4 supporting lines
• For each line: what figures, what statistics, what conclusions

D-Step 2: Define Sufficiency Criteria

IRON LAW: ANALYSIS MUST BE COMPREHENSIVE. NO SHORTCUTS.

Sufficiency checklist — every box must be checked before G2:

• Data explored from multiple angles?
• Main hypothesis tested from multiple perspectives?
• Exploratory analysis planned for unexpected patterns?
• All analyses connect back to story line?
• Statistical support sufficient for each claim?
• Confounders identified and addressed?
• At least 4–6 content points with planned figures/tables?

D-Step 3: Pre-Identify Alternative Explanations

For each expected finding, list plausible alternative explanations that analyses must rule out.

D-Step 4: Multi-Agent Analysis Design Deliberation (AUTOMATED — MANDATORY)

REQUIRED SUB-SKILL: Follow amplify:multi-round-deliberation protocol (max 5 rounds).

Agent composition for Type D:

Dispatch — Round 1 (parallel):

Context package: research question, data description, analysis framework (D-Steps 1-3), sufficiency criteria, alternative explanations table, literature review.

Agent 1 — Domain Scientist:

Call Task tool with:
  description: "Domain Scientist — evaluate analysis plan"
  prompt: |
    SHARED VALUES:
    Target venue: [venue]. Research type: Type D.
    Optimization target: "Will this analysis produce biologically/scientifically meaningful findings?"
    Scoring: PASS / CONDITIONAL / FAIL
    
    You are a domain expert in [SPECIFIC FIELD] with deep knowledge 
    of the biological/scientific context. You know what findings would 
    be genuinely interesting vs. trivially expected.
    
    RESEARCH QUESTION: "[question]"
    DATA: [description]
    ANALYSIS FRAMEWORK: [paste D-Steps 1-3]
    EXPECTED FINDINGS: [paste]
    
    Evaluate:
    1. BIOLOGICAL RELEVANCE: Does the analysis plan target the RIGHT 
       biological questions? Are there more interesting angles being missed?
    2. EXPECTED NOVELTY: If every analysis succeeds, will the findings 
       be genuinely new to the field? Or just confirming known biology?
    3. MISSING ANALYSES: What analyses would a domain expert EXPECT 
       to see in this paper that are not in the plan? Be specific.
    4. INTERPRETATION DEPTH: Will the planned analyses support deep 
       biological interpretation, or just surface-level description?
    5. SUFFICIENCY: Are there enough content points to fill a 
       complete paper at [venue]? Suggest additions if not.
    6. VERDICT: PASS / CONDITIONAL / FAIL
  subagent_type: "generalPurpose"

Agent 2 — Methodology Consultant:

Call Task tool with:
  description: "Methodology Consultant — evaluate analytical approaches"
  prompt: |
    SHARED VALUES:
    Target venue: [venue]. Research type: Type D.
    Optimization target: "Are we using the best available methods for this analysis?"
    Scoring: PASS / CONDITIONAL / FAIL
    
    You are a methods expert familiar with the state-of-the-art 
    analytical tools in [FIELD]. You know which methods are standard, 
    which are cutting-edge, and which are outdated.
    
    ANALYSIS FRAMEWORK: [paste]
    DATA CHARACTERISTICS: [paste]
    TOOLS PLANNED: [paste]
    
    Evaluate:
    1. METHOD APPROPRIATENESS: Are the chosen methods appropriate 
       for the data type and research question? Are there better alternatives?
    2. STATE-OF-THE-ART: Are we using current best practices, or 
       outdated approaches that reviewers will criticize?
    3. METHODOLOGICAL GAPS: Are there analytical techniques from 
       recent literature that could strengthen the findings?
    4. ROBUSTNESS: Are there sufficient cross-validation, sensitivity 
       analyses, and alternative approaches to rule out artifacts?
    5. ADDITIONAL LITERATURE NEEDED: Suggest specific method papers or 
       technique descriptions to review before finalizing.
    6. VERDICT: PASS / CONDITIONAL / FAIL
  subagent_type: "generalPurpose"

Agent 3 — Statistical Rigor Advisor:

Call Task tool with:
  description: "Statistical Advisor — evaluate analysis rigor"
  prompt: |
    SHARED VALUES:
    Target venue: [venue]. Research type: Type D.
    Optimization target: "Will the evidence be statistically convincing?"
    Scoring: PASS / CONDITIONAL / FAIL
    
    You are a statistician/quantitative methodologist who reviews 
    papers for analytical rigor. You catch p-hacking, multiple 
    comparisons problems, insufficient sample sizes, and unjustified 
    statistical claims.
    
    ANALYSIS FRAMEWORK: [paste]
    DATA: [sample sizes, groups, variables]
    SUFFICIENCY CRITERIA: [paste]
    ALTERNATIVE EXPLANATIONS: [paste table]
    
    Evaluate:
    1. STATISTICAL VALIDITY: Are the planned tests appropriate? 
       Are assumptions met? Are multiple comparisons corrected?
    2. CONFOUNDERS: Are all known confounders addressed in the 
       analysis plan? What batch effects, technical artifacts, or 
       demographic variables could confound results?
    3. SAMPLE SIZE: Is the data large enough to detect the 
       expected effects with adequate power?
    4. ALTERNATIVE EXPLANATIONS: Does the plan adequately test 
       the alternative explanations listed? Are any alternatives 
       missing?
    5. REPRODUCIBILITY: Will someone else be able to reproduce 
       these analyses? Are all choices documented?
    6. EXPERIMENT VOLUME: Plan slightly more analyses than strictly 
       needed — better to have extra content to filter than to 
       discover gaps later.
    7. VERDICT: PASS / CONDITIONAL / FAIL
  subagent_type: "generalPurpose"

Multi-round deliberation: Same protocol as Type M — synthesize, refine, search additional literature if flagged, re-dispatch all agents, repeat until convergence or 5 rounds.

Present results to user (same format as Type M deliberation results).

D-Step 5: Confirm Story Line

Present the narrative arc (refined by deliberation) for user approval. Get explicit approval before G2.

Type C Path — Tool / Software

Type C is utility-driven. The contribution is not algorithmic novelty (Type M) or scientific discovery (Type D), but a tool that solves a real problem better than existing alternatives — faster, more usable, more scalable, or covering an unmet need.

C-Step 1: Define the Utility Claim

State precisely what the tool does better than alternatives:

• Primary claim: "[Tool] enables [task] that was previously [impossible / slow / manual / error-prone]"
• Quantitative targets (at least 2):
  • Speed: X× faster than [competitor] on [benchmark]
  • Scalability: handles [scale] that [competitor] cannot
  • Accuracy/quality: matches or exceeds [competitor] on [benchmark]
  • Usability: reduces [task] from N steps to M steps

C-Step 2: Design Evaluation Framework

Tool papers need a DIFFERENT evaluation from method papers:

Record in docs/03_plan/evaluation-protocol.yaml (adapted for tool evaluation).

C-Step 3: Identify Competing Tools

List ALL existing tools that address the same or similar problem:

This becomes the comparison table in the paper.

C-Step 4: Multi-Agent Tool Design Deliberation (AUTOMATED — MANDATORY)

REQUIRED SUB-SKILL: Follow amplify:multi-round-deliberation protocol (max 5 rounds).

Agent composition for Type C:

All three agents get: tool description, API design, evaluation plan, competing tools list.

Each agent evaluates: utility, completeness, comparison fairness, documentation quality.

Present deliberation results to user, then proceed to G2.

C-Step 5: Confirm Story Line

Present the narrative arc for user approval:

Problem (user pain) → Why existing tools fail → Our tool's approach → Benchmark results → Real-world case studies

Type H Path — Hybrid

Execute both Type M and Type D tracks. Before starting, ask user: "Which track is primary — the method contribution or the discovery contribution?" Mark the answer in research-anchor.yaml under primary_track.

For Type H, treat ALL of these as mandatory:

• amplify:evaluation-protocol-design
• amplify:analysis-storyboard-design
• M-Step 5 (Method Design Deliberation) for the method component
• D-Step 4 (Analysis Design Deliberation) for the discovery component

The two deliberations can run sequentially (primary track first) or, if independent, in parallel.

G2 Gate Checklist — Plan Freeze

ALL applicable items must be satisfied. Present this checklist to the user for sign-off.

Type M items:

• evaluation-protocol.yaml locked
• Innovation method fully argued, innovation_point marked
• Baselines confirmed with sources
• Ablation plan documented
• Failure modes predicted with backup plans for each

Type D items:

• Analysis framework and storyboard frozen
• Sufficiency criteria defined and all boxes checked
• Alternative explanations pre-identified

Type C items:

• Utility claim stated with quantitative targets
• Evaluation framework defined (correctness, performance, scalability, comparison)
• Competing tools identified and compared
• Case studies planned
• Documentation plan in place

Universal items:

• Story line confirmed by user
• value_proposition written in research-anchor.yaml
• Venue target still reasonable (invoke venue-alignment check)
• User approved everything explicitly

Only after ALL applicable items pass: set G2 status to passed and proceed to execution phase.

Common Rationalizations

Red Flags — STOP Immediately

• Writing implementation code before G2 passes
• Choosing metrics without user discussion
• Skipping baselines "because the method is different"
• Starting Type D analysis without sufficiency criteria
• Merging Type H tracks without marking a primary
• Proceeding without explicit user approval on story line

Checklist

1. Read research_type from research-anchor.yaml
2. Branch to correct path (M / D / H)
3. Complete all steps for the applicable path
4. Present G2 gate checklist to user
5. Get explicit user approval on every item
6. Mark G2 as passed — proceed to experiment-execution

After presenting the G2 gate checklist, END YOUR RESPONSE IMMEDIATELY.

Do NOT invoke experiment-execution in this same response. Do NOT begin implementing code, downloading data, or setting up experiments. Do NOT proceed to G3 check.

STOP. WAIT. The user must approve the frozen plan before any execution begins.

Your final output should be the G2 checklist followed by: "G2 gate checklist is above. Plan is frozen. Do you approve proceeding to Phase 4 (Experiment Execution)?"

Then STOP. </IRON-LAW>