dsh-aris-panel 0.1.0

package/skills/paper-figure/SKILL.md

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+---
+name: paper-figure
+description: "Generate publication-quality figures and tables from experiment results. Use when user says \"画图\", \"作图\", \"generate figures\", \"paper figures\", or needs plots for a paper."
+argument-hint: "[figure-plan-or-data-path]"
+allowed-tools: Bash(*), Read, Write, Edit, Grep, Glob, mcp__codex__codex, mcp__codex__codex-reply
+---
+
+# Paper Figure: Publication-Quality Plots from Experiment Data
+
+Generate all figures and tables for a paper based on: **$ARGUMENTS**
+
+## Scope: What This Skill Can and Cannot Do
+
+| Category | Can auto-generate? | Examples |
+|----------|-------------------|----------|
+| **Data-driven plots** | ✅ Yes | Line plots (training curves), bar charts (method comparison), scatter plots, heatmaps, box/violin plots |
+| **Comparison tables** | ✅ Yes | LaTeX tables comparing prior bounds, method features, ablation results |
+| **Multi-panel figures** | ✅ Yes | Subfigure grids combining multiple plots (e.g., 3×3 dataset × method) |
+| **Architecture/pipeline diagrams** | ❌ No — manual | Model architecture, data flow diagrams, system overviews. At best can generate a rough TikZ skeleton, but **expect to draw these yourself** using tools like draw.io, Figma, or TikZ |
+| **Generated image grids** | ❌ No — manual | Grids of generated samples (e.g., GAN/diffusion outputs). These come from running your model, not from this skill |
+| **Photographs / screenshots** | ❌ No — manual | Real-world images, UI screenshots, qualitative examples |
+
+**In practice:** For a typical ML paper, this skill handles ~60% of figures (all data plots + tables). The remaining ~40% (hero figure, architecture diagram, qualitative results) need to be created manually and placed in `figures/` before running `/paper-write`. The skill will detect these as "existing figures" and preserve them.
+
+## Constants
+
+- **STYLE = `publication`** — Visual style preset. Options: `publication` (default, clean for print), `poster` (larger fonts), `slide` (bold colors)
+- **DPI = 300** — Output resolution
+- **FORMAT = `pdf`** — Output format. Options: `pdf` (vector, best for LaTeX), `png` (raster fallback)
+- **COLOR_PALETTE = `tab10`** — Default matplotlib color cycle. Options: `tab10`, `Set2`, `colorblind` (deuteranopia-safe)
+- **FONT_SIZE = 10** — Base font size (matches typical conference body text)
+- **FIG_DIR = `figures/`** — Output directory for generated figures
+- **REVIEWER_MODEL = `gpt-5.6-sol`** — Model used via Codex MCP for figure quality review.
+
+## Inputs
+
+1. **PAPER_PLAN.md** — figure plan table (from `/paper-plan`)
+2. **Experiment data** — JSON files, CSV files, or screen logs in `figures/` or project root
+3. **Existing figures** — any manually created figures to preserve
+
+If no PAPER_PLAN.md exists, scan for data files and ask the user which figures to generate.
+
+## Workflow
+
+### Step 1: Read Figure Plan
+
+Parse the Figure Plan table from PAPER_PLAN.md:
+
+```markdown
+| ID | Type | Description | Data Source | Priority |
+|----|------|-------------|-------------|----------|
+| Fig 1 | Architecture | ... | manual | HIGH |
+| Fig 2 | Line plot | ... | figures/exp.json | HIGH |
+```
+
+Identify:
+- Which figures can be auto-generated from data
+- Which need manual creation (architecture diagrams, etc.)
+- Which are comparison tables (generate as LaTeX)
+
+### Step 2: Set Up Plotting Environment
+
+Create a shared style configuration script:
+
+```python
+# paper_plot_style.py — shared across all figure scripts
+import matplotlib.pyplot as plt
+import matplotlib
+matplotlib.rcParams.update({
+    'font.size': FONT_SIZE,
+    'font.family': 'serif',
+    'font.serif': ['Times New Roman', 'Times', 'DejaVu Serif'],
+    'axes.labelsize': FONT_SIZE,
+    'axes.titlesize': FONT_SIZE + 1,
+    'xtick.labelsize': FONT_SIZE - 1,
+    'ytick.labelsize': FONT_SIZE - 1,
+    'legend.fontsize': FONT_SIZE - 1,
+    'figure.dpi': DPI,
+    'savefig.dpi': DPI,
+    'savefig.bbox': 'tight',
+    'savefig.pad_inches': 0.05,
+    'axes.grid': False,
+    'axes.spines.top': False,
+    'axes.spines.right': False,
+    'text.usetex': False,  # set True if LaTeX is available
+    'mathtext.fontset': 'stix',
+})
+
+# Color palette
+COLORS = plt.cm.tab10.colors  # or Set2, or colorblind-safe
+
+def save_fig(fig, name, fmt=FORMAT):
+    """Save figure to FIG_DIR with consistent naming."""
+    fig.savefig(f'{FIG_DIR}/{name}.{fmt}')
+    print(f'Saved: {FIG_DIR}/{name}.{fmt}')
+```
+
+### Step 3: Auto-Select Figure Type
+
+Use this decision tree for data-driven figures (inspired by Imbad0202/academic-research-skills):
+
+| Data Pattern | Recommended Type | Size |
+|-------------|-----------------|------|
+| X=time/steps, Y=metric | Line plot | 0.48\textwidth |
+| Methods × 1 metric | Bar chart | 0.48\textwidth |
+| Methods × multiple metrics | Grouped bar / radar | 0.95\textwidth |
+| Two continuous variables | Scatter plot | 0.48\textwidth |
+| Matrix / grid values | Heatmap | 0.48\textwidth |
+| Distribution comparison | Box/violin plot | 0.48\textwidth |
+| Multi-dataset results | Multi-panel (subfigure) | 0.95\textwidth |
+| Prior work comparison | LaTeX table | — |
+
+### Step 4: Generate Each Figure
+
+For each figure in the plan, create a standalone Python script:
+
+**Line plots** (training curves, scaling):
+```python
+# gen_fig2_training_curves.py
+from paper_plot_style import *
+import json
+
+with open('figures/exp_results.json') as f:
+    data = json.load(f)
+
+fig, ax = plt.subplots(1, 1, figsize=(5, 3.5))
+ax.plot(data['steps'], data['fac_loss'], label='Factorized', color=COLORS[0])
+ax.plot(data['steps'], data['crf_loss'], label='CRF-LR', color=COLORS[1])
+ax.set_xlabel('Training Steps')
+ax.set_ylabel('Cross-Entropy Loss')
+ax.legend(frameon=False)
+save_fig(fig, 'fig2_training_curves')
+```
+
+**Bar charts** (comparison, ablation):
+```python
+fig, ax = plt.subplots(1, 1, figsize=(5, 3))
+methods = ['Baseline', 'Method A', 'Method B', 'Ours']
+values = [82.3, 85.1, 86.7, 89.2]
+bars = ax.bar(methods, values, color=[COLORS[i] for i in range(len(methods))])
+ax.set_ylabel('Accuracy (%)')
+# Add value labels on bars
+for bar, val in zip(bars, values):
+    ax.text(bar.get_x() + bar.get_width()/2, bar.get_height() + 0.3,
+            f'{val:.1f}', ha='center', va='bottom', fontsize=FONT_SIZE-1)
+save_fig(fig, 'fig3_comparison')
+```
+
+**Comparison tables** (LaTeX, for theory papers):
+```latex
+\begin{table}[t]
+\centering
+\caption{Comparison of estimation error bounds. $n$: sample size, $D$: ambient dim, $d$: latent dim, $K$: subspaces, $n_k$: modes.}
+\label{tab:bounds}
+\begin{tabular}{lccc}
+\toprule
+Method & Rate & Depends on $D$? & Multi-modal? \\
+\midrule
+\citet{MinimaxOkoAS23} & $n^{-s'/D}$ & Yes (curse) & No \\
+\citet{ScoreMatchingdistributionrecovery} & $n^{-2/d}$ & No & No \\
+\textbf{Ours} & $\sqrt{\sum n_k d_k / n}$ & No & Yes \\
+\bottomrule
+\end{tabular}
+\end{table}
+```
+
+**Architecture/pipeline diagrams** (MANUAL — outside this skill's scope):
+- These require manual creation using draw.io, Figma, Keynote, or TikZ
+- This skill can generate a rough TikZ skeleton as a starting point, but **do not expect publication-quality results**
+- If the figure already exists in `figures/`, preserve it and generate only the LaTeX `\includegraphics` snippet
+- Flag as `[MANUAL]` in the figure plan and `latex_includes.tex`
+
+### Step 5: Run All Scripts
+
+```bash
+# Run all figure generation scripts
+for script in gen_fig*.py; do
+    python "$script"
+done
+```
+
+Verify all output files exist and are non-empty. Then **render-then-verify**:
+re-open each RENDERED PDF/PNG (not the script) and self-check — no clipped
+labels, no legend covering data, every number/label readable at final print
+size. This self-check happens BEFORE the Step 7 review, so the reviewer's
+budget goes to substance, not to catching clipped axes.
+
+### Step 6: Generate LaTeX Include Snippets
+
+For each figure, output the LaTeX code to include it:
+
+```latex
+% === Fig 2: Training Curves ===
+\begin{figure}[t]
+    \centering
+    \includegraphics[width=0.48\textwidth]{figures/fig2_training_curves.pdf}
+    \caption{Training curves comparing factorized and CRF-LR denoising.}
+    \label{fig:training_curves}
+\end{figure}
+```
+
+Save all snippets to `figures/latex_includes.tex` for easy copy-paste into the paper.
+
+### Step 7: Figure Quality Review with REVIEWER_MODEL
+
+Send figure descriptions and captions to GPT-5.6-Sol for review:
+
+```
+mcp__codex__codex:
+  model: gpt-5.6-sol
+  config: {"model_reasoning_effort": "xhigh"}
+  prompt: |
+    Review these figure/table plans for a [VENUE] submission.
+
+    For each figure:
+    1. Is the caption informative and self-contained?
+    2. Does the figure type match the data being shown?
+    3. Is the comparison fair and clear?
+    4. Any missing baselines or ablations?
+    5. Would a different visualization be more effective?
+
+    [list all figures with captions and descriptions]
+```
+
+### Step 8: Quality Checklist
+
+The checklist is PARTITIONED (pattern from Anthropic's Claude Science
+`figure-style` skill, Apache-2.0): **correctness rules always bind** — they are
+about whether the figure tells the truth, have no aesthetic content, and no
+style choice may override them; **guidance rules are defaults** — they produce
+a clean result, but a deliberate, stated alternative may override them.
+
+**Correctness — always binds, verify against the DATA before the render:**
+
+- [ ] **Excluded data never enters summaries** — a row excluded/flagged in the
+      source either disappears entirely or is drawn visibly distinct (open /
+      hatched marker, named in the key); it never feeds a mean/CI plotted
+      alongside included rows
+- [ ] **Captions and any claim-like title text are tested against EVERY plotted
+      row** — if one category contradicts the claim, qualify it ("on 3 of 4
+      benchmarks") or downgrade to a description; a figure that overclaims is
+      wrong even if it renders beautifully
+- [ ] **Comparable conditions only** — arms measured under different N / budget
+      / protocol are not drawn as visual peers; separate them or mark the
+      difference in the caption
+- [ ] **State n and what was held fixed** — every panel with a summary mark
+      says n and the unit of replication (panel or caption)
+- [ ] **Render-then-verify** — the Step-5 self-check on the RENDERED PDF/PNG
+      (not the script) actually happened: no clipped labels, no legend covering
+      data, every number/label readable at final print size
+
+**Guidance — strong defaults (from pedrohcgs/claude-code-my-workflow), a
+deliberate stated alternative may override — EXCEPT items that Key Rules below
+make hard (vector-PDF output and no-titles-inside-figures are Key Rules: treat
+those two as binding, not overridable):**
+
+- [ ] Font size readable at printed paper size (not too small)
+- [ ] Colors distinguishable in grayscale (print-friendly)
+- [ ] **No title inside figures** — titles go only in LaTeX `\caption{}` (from pedrohcgs)
+- [ ] Legend does not overlap data
+- [ ] Axis labels have units where applicable
+- [ ] Axis labels are publication-quality (not variable names like `emp_rate`)
+- [ ] Figure width fits single column (0.48\textwidth) or full width (0.95\textwidth)
+- [ ] PDF output is vector (not rasterized text)
+- [ ] No matplotlib default title (remove `plt.title` for publications)
+- [ ] Serif font matches paper body text (Times / Computer Modern)
+- [ ] Colorblind-accessible (if using colorblind palette)
+
+## Output
+
+```
+figures/
+├── paper_plot_style.py          # shared style config
+├── gen_fig1_architecture.py     # per-figure scripts
+├── gen_fig2_training_curves.py
+├── gen_fig3_comparison.py
+├── fig1_architecture.pdf        # generated figures
+├── fig2_training_curves.pdf
+├── fig3_comparison.pdf
+├── latex_includes.tex           # LaTeX snippets for all figures
+└── TABLE_*.tex                  # standalone table LaTeX files
+```
+
+## Key Rules
+
+- **Every figure must be reproducible** — save the generation script alongside the output
+- **Do NOT hardcode data** — always read from JSON/CSV files
+- **Use vector format (PDF)** for all plots — PNG only as fallback
+- **No decorative elements** — no background colors, no 3D effects, no chart junk
+- **Consistent style across all figures** — same fonts, colors, line widths
+- **Colorblind-safe** — verify with https://davidmathlogic.com/colorblind/ if needed
+- **One script per figure** — easy to re-run individual figures when data changes
+- **No titles inside figures** — captions are in LaTeX only
+- **Comparison tables count as figures** — generate them as standalone .tex files
+
+## Figure Type Reference
+
+| Type | When to Use | Typical Size |
+|------|------------|--------------|
+| Line plot | Training curves, scaling trends | 0.48\textwidth |
+| Bar chart | Method comparison, ablation | 0.48\textwidth |
+| Grouped bar | Multi-metric comparison | 0.95\textwidth |
+| Scatter plot | Correlation analysis | 0.48\textwidth |
+| Heatmap | Attention, confusion matrix | 0.48\textwidth |
+| Box/violin | Distribution comparison | 0.48\textwidth |
+| Architecture | System overview | 0.95\textwidth |
+| Multi-panel | Combined results (subfigures) | 0.95\textwidth |
+| Comparison table | Prior bounds vs. ours (theory) | full width |
+
+## Acknowledgements
+
+Design pattern (type × style matrix) inspired by [baoyu-skills](https://github.com/jimliu/baoyu-skills). Publication style defaults and figure rules from [pedrohcgs/claude-code-my-workflow](https://github.com/pedrohcgs/claude-code-my-workflow). Visualization decision tree from [Imbad0202/academic-research-skills](https://github.com/Imbad0202/academic-research-skills).