mindforge-cc 11.5.0 → 11.6.0

package/.agent/skills/research-paper-writing/references/experiment-patterns.md

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+# Experiment Design Patterns
+
+Patterns and best practices distilled from running research experiments at scale with the 
+
+---
+
+## Experiment Infrastructure
+
+### Directory Structure
+
+Organize experiments with a consistent structure:
+
+```
+workspace/
+  experiments/
+    run_main.py                # Core experiment runner
+    run_baselines.py           # Baseline comparison
+    run_ablation.py            # Ablation studies
+    strategies.py              # Method implementations
+    config.yaml                # Shared configuration
+  results/
+    <experiment_name>/
+      <task_or_problem>/
+        <strategy>/
+          result.json          # Final metrics
+          final_output.md      # Final output artifact
+          history.json         # Full trajectory/log
+          pass_01/             # Per-iteration artifacts (if iterative)
+            intermediate.md
+  analysis/
+    analyze_results.py         # Statistical analysis
+    compute_stats.py           # Significance tests
+    make_charts.py             # Visualization
+  paper/
+    paper.tex                  # LaTeX source
+    fig_*.pdf                  # Generated figures
+```
+
+### Script Design Principles
+
+**1. Incremental Saving (Crash Recovery)**
+
+Every experiment script should save results after each unit of work, and skip already-completed work on restart:
+
+```python
+import json, os
+from pathlib import Path
+
+def run_experiment(problems, strategies, output_dir):
+    for problem in problems:
+        for strategy in strategies:
+            result_path = Path(output_dir) / problem["id"] / strategy / "result.json"
+            if result_path.exists():
+                print(f"Skipping {problem['id']}/{strategy} (already done)")
+                continue
+            
+            # Run the experiment
+            result = execute_strategy(problem, strategy)
+            
+            # Save immediately
+            result_path.parent.mkdir(parents=True, exist_ok=True)
+            with open(result_path, 'w') as f:
+                json.dump(result, f, indent=2)
+```
+
+This pattern makes re-runs safe and efficient. If a process crashes at problem 47/150, restarting skips the first 46.
+
+**2. Artifact Preservation**
+
+Save all intermediate outputs, not just final results. This enables post-hoc analysis without re-running:
+
+```python
+def save_pass_artifacts(output_dir, pass_num, artifacts):
+    """Save all artifacts from a single pass of an iterative method."""
+    pass_dir = Path(output_dir) / f"pass_{pass_num:02d}"
+    pass_dir.mkdir(parents=True, exist_ok=True)
+    
+    for name, content in artifacts.items():
+        with open(pass_dir / f"{name}.md", 'w') as f:
+            f.write(content)
+```
+
+**3. Configuration Management**
+
+Use YAML configs for reproducibility:
+
+```yaml
+# config.yaml
+model: anthropic/claude-sonnet-4-20250514
+author_temperature: 0.8
+judge_temperature: 0.3
+max_tokens: 4096
+num_judges: 3
+max_passes: 15
+convergence_k: 2
+```
+
+```python
+import yaml
+
+with open("config.yaml") as f:
+    config = yaml.safe_load(f)
+```
+
+**4. Separation of Concerns**
+
+Keep generation, evaluation, and visualization in separate scripts:
+
+| Script | Purpose |
+|--------|---------|
+| `run_experiment.py` | Core method execution |
+| `run_baselines.py` | Baseline comparisons at same compute |
+| `run_eval.py` | Blind evaluation / judge panels |
+| `analyze_results.py` | Statistical analysis |
+| `make_charts.py` | Figure generation |
+
+This lets you re-run evaluation without re-running expensive generation, and regenerate figures without re-running analysis.
+
+---
+
+## Evaluation Protocols
+
+### Blind Judge Panels (for Subjective Tasks)
+
+When evaluating subjective outputs (writing, analysis, recommendations), use a blind judge panel:
+
+```python
+import random
+
+def run_blind_evaluation(outputs: dict, task_prompt: str, num_judges: int = 7):
+    """
+    Run blind evaluation of multiple method outputs.
+    
+    Args:
+        outputs: {"method_name": "output_text", ...}
+        task_prompt: The original task description
+        num_judges: Number of independent judge evaluations
+    """
+    rankings = []
+    
+    for judge_i in range(num_judges):
+        # Randomize labels and presentation order per judge
+        methods = list(outputs.keys())
+        random.shuffle(methods)
+        labels = {m: chr(65 + i) for i, m in enumerate(methods)}  # A, B, C...
+        
+        # Present to judge with randomized labels
+        prompt = f"Task: {task_prompt}\n\n"
+        for method in methods:
+            prompt += f"--- Proposal {labels[method]} ---\n{outputs[method]}\n\n"
+        prompt += "Rank all proposals from best to worst. Format: RANKING: [best], [second], [worst]"
+        
+        ranking = call_judge(prompt)
+        rankings.append({"labels": labels, "ranking": ranking})
+    
+    # Aggregate via Borda count
+    return compute_borda(rankings)
+
+def compute_borda(rankings, n_methods=3):
+    """Borda count: 3/2/1 points for 1st/2nd/3rd."""
+    scores = {}
+    points = {0: n_methods, 1: n_methods - 1, 2: n_methods - 2}  # Adjust for n_methods
+    
+    for r in rankings:
+        for position, method in enumerate(r["ranking"]):
+            scores[method] = scores.get(method, 0) + points.get(position, 0)
+    
+    return scores
+```
+
+Key design decisions:
+- **Randomize both labels AND order** per judge to prevent position bias
+- **Use odd number of judges** (3, 5, 7) to break ties
+- **Conservative tiebreak**: Incumbent/baseline wins ties (prevents false positives)
+- **CoT judges** match non-CoT quality at ~40% cost (1 CoT judge ≈ 3 standard judges)
+
+### Code/Objective Evaluation
+
+For tasks with ground-truth evaluation (code, math, factual):
+
+```python
+import subprocess
+
+def evaluate_code(solution: str, test_cases: list, timeout: int = 30):
+    """Run code solution against test cases with sandboxed execution."""
+    results = {"public": [], "private": []}
+    
+    for test in test_cases:
+        try:
+            proc = subprocess.run(
+                ["python3", "-c", solution],
+                input=test["input"],
+                capture_output=True,
+                timeout=timeout,
+                text=True
+            )
+            actual = proc.stdout.strip()
+            expected = test["expected"].strip()
+            passed = actual == expected
+        except subprocess.TimeoutExpired:
+            passed = False
+        
+        category = "public" if test.get("public") else "private"
+        results[category].append(passed)
+    
+    return {
+        "public_pass_rate": sum(results["public"]) / max(len(results["public"]), 1),
+        "private_pass_rate": sum(results["private"]) / max(len(results["private"]), 1),
+    }
+```
+
+### Compute-Matched Comparison
+
+Always compare methods at equal compute budget. If your method uses N API calls, baselines get N calls too:
+
+| Method | Call Budget | Allocation |
+|--------|-----------|------------|
+| Single pass | 6 calls | 6 independent generations |
+| Critique & revise | 6 calls | 1 generate + 5 revise rounds |
+| Autoreason | 6 calls | 1 generate + 1 analysis + 4 revisions |
+| Best-of-N | 6 calls | 6 independent, pick best on public test |
+
+### Human Evaluation Design
+
+Many ML/NLP papers require human evaluation, especially for subjective tasks (text generation, summarization, dialogue, creative writing). Poorly designed human evals are a common rejection reason.
+
+#### When Human Evaluation Is Required
+
+| Task Type | Required? | Notes |
+|-----------|-----------|-------|
+| Text generation (open-ended) | Yes | LLM-as-judge alone is insufficient for acceptance at ACL/EMNLP |
+| Summarization | Usually | At minimum for a subset of outputs |
+| Dialogue systems | Yes | User studies or annotation |
+| Code generation | No | Test suites are objective ground truth |
+| Classification | No | Standard metrics suffice |
+| Any task with subjective quality | Strongly recommended | Strengthens the paper significantly |
+
+#### Annotation Protocol Design
+
+```
+Human Evaluation Protocol:
+1. Define the evaluation dimensions (fluency, relevance, factual accuracy, etc.)
+2. Create annotation guidelines with examples of each score level
+3. Run a pilot with 2-3 annotators on 20-30 examples
+4. Compute pilot inter-annotator agreement — if low, revise guidelines
+5. Run full evaluation
+6. Report: annotator count, agreement metrics, compensation, time per item
+```
+
+**Evaluation dimensions** (pick relevant subset):
+
+| Dimension | Definition | Scale |
+|-----------|-----------|-------|
+| Fluency | Grammaticality and naturalness | 1-5 Likert |
+| Relevance | Does it address the task? | 1-5 Likert |
+| Factual accuracy | Are stated facts correct? | Binary or 1-5 |
+| Coherence | Logical flow and consistency | 1-5 Likert |
+| Informativeness | Does it provide useful information? | 1-5 Likert |
+| Overall preference | Which output is better? | A/B/Tie (pairwise) |
+
+**Pairwise comparison** (preferred over absolute scoring — more reliable):
+- Present two outputs side-by-side (randomize left/right position)
+- Ask: "Which is better? A / B / Tie"
+- More discriminative and less susceptible to annotator calibration drift
+
+#### Inter-Annotator Agreement
+
+Always report agreement metrics. Without them, reviewers assume your annotations are unreliable.
+
+```python
+# Krippendorff's alpha (preferred — handles missing data, any scale)
+# pip install krippendorffs-alpha
+import krippendorff
+
+# Ratings: rows = annotators, columns = items, values = scores
+ratings = [
+    [3, 4, 1, 2, 5, None, 3],  # Annotator 1
+    [3, 5, 1, 3, 5, 2, 3],     # Annotator 2
+    [4, 4, 2, 2, 4, 2, None],  # Annotator 3
+]
+alpha = krippendorff.alpha(reliability_data=ratings, level_of_measurement="ordinal")
+print(f"Krippendorff's alpha: {alpha:.3f}")
+# Interpretation: >0.80 good, 0.67-0.80 acceptable, <0.67 questionable
+```
+
+```python
+# Cohen's kappa (for exactly 2 annotators, categorical data)
+from sklearn.metrics import cohen_kappa_score
+
+annotator_1 = [1, 2, 3, 1, 2, 3, 2]
+annotator_2 = [1, 2, 2, 1, 3, 3, 2]
+kappa = cohen_kappa_score(annotator_1, annotator_2)
+print(f"Cohen's kappa: {kappa:.3f}")
+# Interpretation: >0.80 excellent, 0.60-0.80 substantial, 0.40-0.60 moderate
+```
+
+| Metric | When to Use | Annotators | Scale |
+|--------|------------|-----------|-------|
+| Krippendorff's alpha | Default choice | Any number | Any (ordinal, nominal, ratio) |
+| Cohen's kappa | 2 annotators, categorical | Exactly 2 | Nominal/ordinal |
+| Fleiss' kappa | 3+ annotators, categorical | 3+ | Nominal |
+| Pearson/Spearman | Continuous scores | 2 | Interval/ratio |
+
+#### Crowdsourcing Platforms
+
+| Platform | Best For | Cost | Quality |
+|----------|----------|------|---------|
+| **Prolific** | Academic research, higher quality | $8-15/hr | High — academic participant pool |
+| **MTurk** | Large-scale, fast turnaround | $2-10/hr | Variable — use qualifications |
+| **Surge AI** | NLP-specific annotations | Premium | High — trained annotators |
+| **Expert annotators** | Domain-specific (medical, legal) | Highest | Highest — but slow |
+
+**Ethics requirements**:
+- Report compensation rate (must be at minimum local minimum wage)
+- Describe annotator demographics if relevant
+- Obtain IRB/ethics approval if required by your institution
+- ACL venues explicitly require compensation documentation
+
+#### What to Report in the Paper
+
+```
+Human Evaluation Section Checklist:
+- [ ] Number of annotators
+- [ ] Annotator qualifications / recruitment method
+- [ ] Number of items evaluated
+- [ ] Evaluation dimensions with definitions
+- [ ] Scale used (Likert, pairwise, binary)
+- [ ] Inter-annotator agreement (Krippendorff's alpha or Cohen's kappa)
+- [ ] Compensation rate
+- [ ] Time per annotation item
+- [ ] Whether annotators saw model identities (should be blind)
+- [ ] Randomization of presentation order
+```
+
+---
+
+## Statistical Analysis
+
+### Required Tests
+
+| Test | When to Use | Python |
+|------|------------|--------|
+| McNemar's test | Comparing two methods on same problems | `scipy.stats.binomtest` for small n |
+| Two-proportion z-test | Comparing success rates | Custom or `statsmodels` |
+| Fisher's exact test | Small sample pairwise comparison | `scipy.stats.fisher_exact` |
+| Bootstrapped CI | Confidence intervals for any metric | Custom bootstrap |
+| Cohen's h | Effect size for proportions | Manual calculation |
+
+### Standard Analysis Script
+
+```python
+import numpy as np
+from scipy import stats
+from pathlib import Path
+import json
+
+def load_all_results(results_dir):
+    """Load all results into a structured format."""
+    results = {}
+    for result_file in Path(results_dir).rglob("result.json"):
+        parts = result_file.relative_to(results_dir).parts
+        if len(parts) >= 3:
+            experiment, task, strategy = parts[0], parts[1], parts[2]
+            data = json.loads(result_file.read_text())
+            results.setdefault(experiment, {}).setdefault(strategy, {})[task] = data
+    return results
+
+def pairwise_mcnemar(method_a_results, method_b_results):
+    """McNemar's test for paired binary outcomes."""
+    a_win_b_lose = sum(1 for a, b in zip(method_a_results, method_b_results) if a and not b)
+    b_win_a_lose = sum(1 for a, b in zip(method_a_results, method_b_results) if b and not a)
+    
+    n = a_win_b_lose + b_win_a_lose
+    if n < 25:
+        # Use exact binomial for small samples
+        result = stats.binomtest(a_win_b_lose, n, 0.5)
+        p_value = result.pvalue
+    else:
+        # Chi-squared approximation
+        chi2 = (abs(a_win_b_lose - b_win_a_lose) - 1)**2 / (a_win_b_lose + b_win_a_lose)
+        p_value = 1 - stats.chi2.cdf(chi2, df=1)
+    
+    return {
+        "a_wins": a_win_b_lose,
+        "b_wins": b_win_a_lose,
+        "n_discordant": n,
+        "p_value": p_value,
+        "significant": p_value < 0.05
+    }
+
+def bootstrap_ci(data, n_bootstrap=10000, ci=0.95):
+    """Bootstrap confidence interval for mean."""
+    means = []
+    for _ in range(n_bootstrap):
+        sample = np.random.choice(data, size=len(data), replace=True)
+        means.append(np.mean(sample))
+    lower = np.percentile(means, (1 - ci) / 2 * 100)
+    upper = np.percentile(means, (1 + ci) / 2 * 100)
+    return {"mean": np.mean(data), "ci_lower": lower, "ci_upper": upper}
+
+def cohens_h(p1, p2):
+    """Cohen's h effect size for two proportions."""
+    return 2 * np.arcsin(np.sqrt(p1)) - 2 * np.arcsin(np.sqrt(p2))
+```
+
+### Reporting Standards
+
+Always include in the paper:
+- **Sample sizes**: n=X problems/tasks
+- **Number of runs**: K independent runs if applicable
+- **Error bars**: Specify standard deviation or standard error
+- **Confidence intervals**: 95% CI for key results
+- **Significance tests**: p-values for key comparisons
+- **Effect sizes**: Cohen's d or h for practical significance
+
+---
+
+## Monitoring (Cron Pattern)
+
+### Cron Prompt Template
+
+For each experiment batch, create a monitoring prompt:
+
+```
+Check the status of the [EXPERIMENT_NAME] experiment:
+
+1. Process check: ps aux | grep [PROCESS_PATTERN]
+2. Log check: tail -30 [LOG_FILE]
+3. Results check: ls [RESULT_DIR]/eval/ (or appropriate result location)
+4. If results are available:
+   - Read the result JSON files
+   - Report metrics in a table (Borda scores, accuracy, etc.)
+   - Compute key comparisons between methods
+5. If all experiments in this batch are complete:
+   - git add -A && git commit -m "[COMMIT_MESSAGE]" && git push
+   - Report final summary
+6. Key question: [SPECIFIC ANALYTICAL QUESTION]
+
+If nothing has changed since the last check, respond with [SILENT].
+```
+
+### Monitoring Best Practices
+
+1. **Check processes first** — don't read results if the experiment is still running and results are incomplete
+2. **Read the log tail** — look for errors, progress indicators, completion messages
+3. **Count completed vs expected** — "45/150 problems done" is more useful than "some results exist"
+4. **Report in structured tables** — always include key metrics in a table
+5. **Answer the key question** — each experiment should have a specific analytical question to answer when done
+6. **[SILENT] for no-news** — suppress notifications when nothing has changed
+7. **Commit on completion** — every completed batch gets committed with a descriptive message
+
+### Example Monitoring Report
+
+```
+## Code Experiments (Haiku 3.5) - COMPLETE
+
+| Strategy | Pass Rate (150 problems) | vs Single |
+|----------|------------------------|-----------|
+| single_pass | 38.0% | — |
+| critique_revise | 35.2% | -2.8pp |
+| **autoreason** | **40.0%** | **+2.0pp** |
+| best_of_6 | 31.0% | -7.0pp |
+
+Key finding: Autoreason shows +2pp improvement over single pass, while 
+best-of-6 collapses due to single-public-test selection issue.
+
+Committed: `git commit -m "Add Haiku code results (150 problems, 4 strategies)"`
+Next: Run significance tests on these results.
+```
+
+---
+
+## Failure Recovery
+
+### Common Failures and Recovery
+
+| Failure | Detection | Recovery |
+|---------|-----------|----------|
+| **API credit exhaustion** | 402 errors in logs, incomplete results | Top up credits, re-run (skips completed work automatically) |
+| **Rate limiting** | 429 errors, slow progress | Add retry logic with exponential backoff |
+| **Process crash** | PID gone, log stops mid-problem | Re-run script (resumes from last checkpoint) |
+| **Wrong model ID** | Model not found errors | Fix ID (e.g., `claude-opus-4-6` not `claude-opus-4.6`) |
+| **Parallel slowdown** | Each experiment taking 2x longer | Reduce parallel experiments to 2-3 max |
+| **Security scan blocks** | Commands blocked by security | Use `execute_code` instead of piped `terminal` commands |
+| **Delegation failures** | `delegate_task` returns errors | Fall back to doing work directly |
+| **Timeout on hard problems** | Process stuck, no log progress | Kill, skip problem, note in results |
+| **Dataset path mismatch** | File not found errors | Verify paths before launching |
+
+### Retry Naming Convention
+
+When re-running failed experiments, use a suffix to track rounds:
+
+```
+logs/experiment_haiku_0_50.log       # Round 1
+logs/experiment_haiku_0_50_r2.log    # Round 2 (after credit exhaustion)
+logs/experiment_haiku_0_50_r3.log    # Round 3 (after bug fix)
+```
+
+### Pre-Flight Checklist
+
+Before launching any experiment batch:
+
+```
+Pre-Flight:
+- [ ] API credits sufficient for estimated calls
+- [ ] Model IDs correct (test with 1 problem first)
+- [ ] Output directory exists and is writable
+- [ ] Resume logic works (re-run won't overwrite existing results)
+- [ ] Log file path is unique (won't overwrite previous logs)
+- [ ] Dataset/task files are accessible
+- [ ] Config matches intended experiment
+```
+
+---
+
+## Task/Benchmark Design
+
+### Open-Ended Tasks (Subjective Evaluation)
+
+Design tasks that have clear objectives but subjective quality:
+
+```markdown
+# Task: [Title]
+
+## Context
+[Specific scenario with concrete details: company size, constraints, timeline]
+
+## Deliverable
+[Exact format and structure required]
+
+## Requirements
+- [Specific, measurable requirements]
+- [Not vague — "be comprehensive" is bad, "include exactly 6 sections" is good]
+```
+
+### Constrained Tasks (for Testing Scope Effects)
+
+Constrained tasks test whether methods respect scope boundaries. Design with:
+
+- **Fixed facts**: "Use only these N data points, add nothing else"
+- **Fixed deliverable**: Specific format (pitch, postmortem, memo — not "improve this")
+- **Fixed structure**: "These sections in this order, do not add/remove"
+- **Fixed change items**: "Address exactly these N points, nothing else"
+
+**Do NOT use word count as a scope constraint.** Word limits cause false convergence — outputs get rejected for length, not quality. Constrain scope (what to include) not length.
+
+### Example: Good vs Bad Constraints
+
+| Bad Constraint | Why | Good Constraint |
+|---------------|-----|-----------------|
+| "Max 500 words" | Judges reject for length | "Exactly 4 sections, each with 3 numbered items" |
+| "Be concise" | Too vague | "Each prohibition must reference a specific base fact" |
+| "Improve this" | Unbounded scope | "Write a 600-word incident postmortem with this exact structure" |
+| "Make it better" | No clear criterion | "Address exactly these 3 reviewer concerns" |
+
+---
+
+## Visualization Best Practices
+
+### Setup: SciencePlots + matplotlib
+
+Install SciencePlots for publication-ready defaults:
+
+```bash
+pip install SciencePlots matplotlib numpy
+```
+
+**Option A: SciencePlots styles** (recommended — handles most defaults automatically):
+
+```python
+import matplotlib.pyplot as plt
+import scienceplots  # registers the styles
+
+# Pick a style:
+# 'science'        — clean, serif fonts, suitable for most venues
+# 'science+ieee'   — IEEE-style (good for two-column papers)
+# 'science+nature' — Nature-style
+# Add 'no-latex' if LaTeX is not installed on the machine generating plots
+
+with plt.style.context(['science', 'no-latex']):
+    fig, ax = plt.subplots(figsize=(3.5, 2.5))  # single-column width
+    # ... plot ...
+    fig.savefig('paper/fig_results.pdf', bbox_inches='tight')
+```
+
+**Option B: Manual rcParams** (when you need full control):
+
+```python
+import matplotlib.pyplot as plt
+
+plt.rcParams.update({
+    'font.size': 10,
+    'font.family': 'serif',
+    'axes.labelsize': 11,
+    'axes.titlesize': 11,
+    'xtick.labelsize': 9,
+    'ytick.labelsize': 9,
+    'legend.fontsize': 9,
+    'figure.figsize': (3.5, 2.5),    # single-column default
+    'figure.dpi': 300,
+    'savefig.dpi': 300,
+    'savefig.bbox': 'tight',
+    'savefig.pad_inches': 0.05,
+    'axes.linewidth': 0.8,
+    'lines.linewidth': 1.5,
+    'lines.markersize': 5,
+    'axes.grid': True,
+    'grid.alpha': 0.3,
+    'grid.linewidth': 0.5,
+})
+```
+
+### Standard Figure Sizes (Two-Column Format)
+
+| Use Case | figsize | Notes |
+|----------|---------|-------|
+| Single column | `(3.5, 2.5)` | Fits in one column of two-column layout |
+| Double column | `(7.0, 3.0)` | Spans full page width |
+| Square (heatmap, confusion matrix) | `(3.5, 3.5)` | Single column |
+| Tall single (many rows) | `(3.5, 5.0)` | Use sparingly |
+
+### Colorblind-Safe Palette (Okabe-Ito)
+
+Use this palette for all paper figures. It is distinguishable by people with all common forms of color vision deficiency:
+
+```python
+COLORS = {
+    'blue':    '#0072B2',
+    'orange':  '#E69F00',
+    'green':   '#009E73',
+    'red':     '#D55E00',
+    'purple':  '#CC79A7',
+    'cyan':    '#56B4E9',
+    'yellow':  '#F0E442',
+    'black':   '#000000',
+}
+
+# As a list for cycling:
+COLOR_CYCLE = ['#0072B2', '#D55E00', '#009E73', '#E69F00', '#CC79A7', '#56B4E9']
+```
+
+Also differentiate lines by **marker and linestyle**, not just color:
+```python
+STYLES = [
+    {'color': '#0072B2', 'marker': 'o', 'linestyle': '-'},
+    {'color': '#D55E00', 'marker': 's', 'linestyle': '--'},
+    {'color': '#009E73', 'marker': '^', 'linestyle': '-.'},
+    {'color': '#E69F00', 'marker': 'D', 'linestyle': ':'},
+]
+```
+
+### Complete Example: Method Comparison Bar Chart
+
+```python
+import matplotlib.pyplot as plt
+import numpy as np
+
+try:
+    import scienceplots
+    style = ['science', 'no-latex']
+except ImportError:
+    style = 'default'
+
+with plt.style.context(style):
+    methods = ['Single Pass', 'Critique+Revise', 'Best-of-N', 'Ours']
+    scores = [73.2, 74.1, 68.5, 77.0]
+    errors = [2.1, 1.8, 3.2, 1.5]
+    colors = ['#56B4E9', '#E69F00', '#CC79A7', '#0072B2']
+    
+    fig, ax = plt.subplots(figsize=(3.5, 2.5))
+    bars = ax.bar(methods, scores, yerr=errors, capsize=3,
+                  color=colors, edgecolor='black', linewidth=0.5)
+    
+    # Highlight "Ours"
+    bars[-1].set_edgecolor('#0072B2')
+    bars[-1].set_linewidth(1.5)
+    
+    ax.set_ylabel('Pass Rate (%)')
+    ax.set_ylim(60, 85)
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+    
+    fig.savefig('paper/fig_comparison.pdf', bbox_inches='tight')
+```
+
+### Complete Example: Convergence/Trajectory Line Chart
+
+```python
+with plt.style.context(style):
+    fig, ax = plt.subplots(figsize=(3.5, 2.5))
+    
+    passes = np.arange(1, 16)
+    ours = [65, 72, 78, 82, 85, 87, 88, 89, 89.5, 90, 90, 90, 90, 90, 90]
+    baseline = [65, 68, 70, 71, 69, 67, 66, 65, 64, 63, 62, 61, 60, 59, 58]
+    
+    ax.plot(passes, ours, **STYLES[0], label='Ours', markersize=4)
+    ax.plot(passes, baseline, **STYLES[1], label='Critique+Revise', markersize=4)
+    
+    # Mark convergence point
+    ax.axvline(x=10, color='gray', linestyle=':', alpha=0.5, linewidth=0.8)
+    ax.annotate('Converged', xy=(10, 90), fontsize=8, ha='center',
+                xytext=(10, 93), arrowprops=dict(arrowstyle='->', color='gray'))
+    
+    ax.set_xlabel('Iteration')
+    ax.set_ylabel('Quality Score')
+    ax.legend(loc='lower right')
+    ax.spines['top'].set_visible(False)
+    ax.spines['right'].set_visible(False)
+    
+    fig.savefig('paper/fig_trajectory.pdf', bbox_inches='tight')
+```
+
+### Output Rules
+
+- **Always save as PDF**: `fig.savefig('fig.pdf')` — vector graphics, sharp at any zoom
+- **Never save as PNG** for paper figures — raster PNGs look blurry when printed/zoomed
+- **Exception**: Screenshots, photographs, or pixel-art visualizations → PNG at 600 DPI
+- **Verify grayscale**: Print to grayscale PDF and check all information is still visible
+
+### Chart Types for Common Comparisons
+
+| Comparison Type | Chart | Notes |
+|----------------|-------|-------|
+| Method vs method | Grouped bar chart | Include error bars |
+| Across model sizes | Line chart with CI bands | Log scale for model size axis |
+| Ablation study | Stacked/grouped bar | Highlight removed component |
+| Trajectory/convergence | Line chart over iterations | Show winner per iteration |
+| Per-task breakdown | Heatmap or grouped bar | Show variance across tasks |