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skills/brycewang-stanford/Auto-Empirical-Research-Skills/42-wanshuiyin-aris-skills-skills-codex-experiment-bridge

42-wanshuiyin-aris-skills-skills-codex-experiment-bridge

1
brycewang-stanford/Auto-Empirical-Research-Skills·Research·Audit pending·Snapshot 3b2cf5b08cf9

Summary

This source did not publish a separate summary. Review SKILL.md before using the skill.

SKILL.md

Workflow 1.5: Experiment Bridge

Implement and deploy experiments from plan: $ARGUMENTS

Overview

This skill bridges Workflow 1 (idea discovery + method refinement) and Workflow 2 (auto review loop). It takes the experiment plan and turns it into running experiments with initial results.

Workflow 1 output:                    This skill:                        Workflow 2 input:
refine-logs/EXPERIMENT_PLAN.md   →   implement → deploy → collect   →   initial results ready
refine-logs/EXPERIMENT_TRACKER.md     code        /run-experiment        for /auto-review-loop
refine-logs/FINAL_PROPOSAL.md

Constants

  • AUTO_DEPLOY = true — Automatically deploy experiments after implementation. Set false to review code before deploying.
  • SANITY_FIRST = true — Run the sanity-stage experiment first (smallest, fastest) before launching the rest. Catches setup bugs early.
  • MAX_PARALLEL_RUNS = 4 — Maximum number of experiments to deploy in parallel (limited by available GPUs).
  • BASE_REPO = false — GitHub repo URL to use as a base codebase. When set, clone it first and implement experiments on top of it.
  • COMPACT = false — When true, prefer IDEA_CANDIDATES.md over the full IDEA_REPORT.md, and append completed runs to EXPERIMENT_LOG.md.

Override: /experiment-bridge "EXPERIMENT_PLAN.md" — compact: true, base repo: https://github.com/org/project

Inputs

This skill expects one or more of:

  1. refine-logs/EXPERIMENT_PLAN.md (best) — claim-driven experiment roadmap from /experiment-plan
  2. refine-logs/EXPERIMENT_TRACKER.md — run-by-run execution table
  3. — method description for implementation context
refine-logs/FINAL_PROPOSAL.md
  • IDEA_CANDIDATES.md — compact idea summary (preferred when COMPACT = true)
  • IDEA_REPORT.md — fallback if refine-logs don't exist
  • If none exist, ask the user what experiments to implement.

    Workflow

    Phase 1: Parse the Experiment Plan

    Read EXPERIMENT_PLAN.md and extract:

    1. Run order and milestones — which experiments run first (sanity → baseline → main → ablation → polish)
    2. For each experiment block:
      • Dataset / split / task
      • Compared systems and variants
      • Metrics to compute
      • Setup details (backbone, hyperparameters, seeds)
      • Success criterion
      • Priority (MUST-RUN vs NICE-TO-HAVE)
    3. Compute budget — total estimated GPU-hours
    4. Method details from FINAL_PROPOSAL.md — what exactly to implement

    Present a brief summary:

    📋 Experiment plan loaded:
    - Milestones: [N] (sanity → baseline → main → ablation)
    - Must-run experiments: [N]
    - Nice-to-have: [N]
    - Estimated GPU-hours: [X]
    
    Proceeding to implementation.
    

    Phase 2: Implement Experiment Code

    If BASE_REPO is set — clone the repo first:

    git clone <BASE_REPO> base_repo/
    

    For each milestone (in order), write the experiment scripts:

    1. Check existing code — scan the project (or cloned base_repo/) for existing experiment scripts, model code, and data loaders. Reuse as much as possible.

    2. Implement missing pieces:

      • Training scripts with proper argparse (all hyperparameters configurable)
      • Evaluation scripts computing the specified metrics
      • Data loading / preprocessing if needed
      • Baseline implementations if not already present
      • Fixed random seeds for reproducibility
      • Results saved to JSON/CSV for later analysis
      • Proper logging (wandb if configured in AGENTS.md)
    3. Follow the plan's run order — implement sanity-stage experiments first, then baselines, then main method, then ablations.

    4. Self-review before deploying:

      • Are all hyperparameters from EXPERIMENT_PLAN.md reflected in argparse?
      • Is the random seed fixed and controllable?
      • Are results saved in a parseable format (JSON/CSV)?
      • Does the code match FINAL_PROPOSAL.md's method description?
      • CRITICAL: does evaluation compare predictions against dataset ground truth, never another model's output?

    Phase 3: Sanity Check (if SANITY_FIRST = true)

    Before deploying the full experiment suite, run the sanity-stage experiment:

    /run-experiment [sanity experiment command]
    

    Wait for completion. Verify:

    • Training loop runs without errors
    • Metrics are computed and saved correctly
    • GPU memory usage is within bounds
    • Output format matches expectations

    If sanity fails → fix the code, re-run. Do not proceed to full deployment with broken code.

    Phase 4: Deploy Full Experiments

    Deploy experiments following the plan's milestone order:

    /run-experiment [experiment commands]
    

    For each milestone:

    1. Deploy experiments in parallel (up to MAX_PARALLEL_RUNS)
    2. Use /monitor-experiment to track progress
    3. Collect results as experiments complete

    🚦 Checkpoint (if AUTO_DEPLOY = false):

    🔧 Code implementation complete. Ready to deploy:
    
    Milestone 0 (sanity): [status — passed/pending]
    Milestone 1 (baseline): [N experiments, ~X GPU-hours]
    Milestone 2 (main method): [N experiments, ~X GPU-hours]
    Milestone 3 (ablations): [N experiments, ~X GPU-hours]
    
    Total estimated: ~X GPU-hours on [N] GPUs
    
    Deploy now? Or review the code first?
    

    Phase 5: Collect Initial Results

    As experiments complete:

    1. Parse output files (JSON/CSV/logs) for key metrics
    2. Training quality check — if W&B data is available, invoke /training-check to detect NaN, loss divergence, plateaus, or overfitting. If W&B is not configured, skip silently.
    3. Update refine-logs/EXPERIMENT_TRACKER.md — fill in Status and Notes columns
    4. Check success criteria from EXPERIMENT_PLAN.md — did each experiment meet its bar?
    5. Write initial results summary:
    # Initial Experiment Results
    
    **Date**: [today]
    **Plan**: refine-logs/EXPERIMENT_PLAN.md
    
    ## Results by Milestone
    
    ### M0: Sanity — PASSED
    - [result]
    
    ### M1: Baselines
    | Run | System | Key Metric | Status |
    |-----|--------|-----------|--------|
    | R001 | baseline_1 | X.XX | DONE |
    
    ### M2: Main Method
    | Run | System | Key Metric | Status |
    |-----|--------|-----------|--------|
    | R003 | our_method | X.XX | DONE |
    
    ### M3: Ablations
    ...
    
    ## Summary
    - [X/Y] must-run experiments completed
    - Main result: [positive/negative/inconclusive]
    - Ready for /auto-review-loop: [YES/NO]
    
    ## Next Step
    → /auto-review-loop "[topic]"
    

    Phase 5.5: Write Compact Log (when COMPACT = true)

    Skip entirely if COMPACT is false.

    Append each completed experiment to EXPERIMENT_LOG.md:

    ## [Run ID] — [timestamp]
    - **System**: [method name]
    - **Config**: [key hyperparameters]
    - **Result**: [primary metric = X.XX]
    - **Verdict**: [positive / negative / inconclusive]
    - **Reproduce**: `python train.py --config configs/run_id.yaml --seed 42`
    

    Phase 5.6: Auto Ablation Planning

    After main experiments (M2) complete with positive results, invoke /ablation-planner to design ablation studies:

    • Read the main results and method description
    • Generate a claim-driven ablation plan: which components to remove, what to compare, and expected outcomes
    • Append ablation blocks to refine-logs/EXPERIMENT_PLAN.md and refine-logs/EXPERIMENT_TRACKER.md
    • If main results are negative or inconclusive, skip ablation planning and note that in the summary

    If /ablation-planner is unavailable, skip silently.

    Phase 6: Handoff

    Present final status:

    🔬 Experiment bridge complete:
    - Implemented: [N] experiment scripts
    - Deployed: [N] experiments on [M] GPUs
    - Completed: [X/Y] must-run, [A/B] nice-to-have
    - Main result: [one sentence]
    
    Results: refine-logs/EXPERIMENT_RESULTS.md
    Tracker: refine-logs/EXPERIMENT_TRACKER.md
    
    Ready for Workflow 2:
    → /auto-review-loop "[topic]"
    

    Key Rules

    • Large file handling: If the Write tool fails due to file size, immediately retry using Bash (cat << 'EOF' > file) to write in chunks. Do NOT ask the user for permission — just do it silently.
    • CRITICAL — Evaluation must use dataset ground truth. Always compare model predictions against the dataset's actual labels/targets, never another model's output. If the task has official eval scripts, prefer them.
    • Follow the plan. Do not invent experiments not in EXPERIMENT_PLAN.md. If you think something is missing, note it but don't add it.
    • Sanity first. Never deploy a full suite without verifying the sanity stage passes.
    • Reuse existing code. Scan the project before writing new scripts. Extend, don't duplicate.
    • Save everything as JSON/CSV. The auto-review-loop needs parseable results, not just terminal output.
    • Update the tracker. EXPERIMENT_TRACKER.md should reflect real status after each run completes.
    • Don't wait forever. If an experiment exceeds 2x its estimated time, flag it and move on to the next milestone.
    • Budget awareness. Track GPU-hours against the plan's budget. Warn if approaching the limit.

    Composing with Other Skills

    /idea-discovery "direction"          ← Workflow 1: find + refine + plan
    /experiment-bridge                   ← you are here (Workflow 1.5: implement + deploy)
    /auto-review-loop "topic"            ← Workflow 2: review + iterate
    /paper-writing "NARRATIVE_REPORT.md" ← Workflow 3: write the paper
    
    Or use /research-pipeline for the full end-to-end flow (includes this bridge).
    

    Related skills

    r-reproducibility-guideAnswering Research QuestionsBuilding Paper Screening RubricsChina-CF-StudyCleaning Up Research Sessions