---
name: Section Writing Agent
slug: section-writing-agent
category: AI Engineering
description: Section Writing Agent drafts the remaining paper sections in one multimodal LLM call and merges them into an existing LaTeX template. It is used to fill in Abstract, Methodology, Experiments, and Conclusion from the outline, figures, and experimental log.
github: "https://github.com/Ar9av/PaperOrchestra/tree/main/skills/section-writing-agent"
language: Python
stars: 644
forks: 91
install: "npx degit https://github.com/Ar9av/PaperOrchestra/tree/main/skills/section-writing-agent ~/.claude/skills/section-writing-agent"
installs_to: ~/.claude/skills/section-writing-agent
source_path: skills/section-writing-agent/SKILL.md
collection_size: 9
category_size: 2451
collection_url: "https://dirskills.com/collections/Ar9av/PaperOrchestra"
added: 2026-08-24T05:17:45.591Z
last_synced: 2026-08-24T05:17:45.591Z
canonical_url: "https://dirskills.com/skills/section-writing-agent"
---

# Section Writing Agent

Section Writing Agent drafts the remaining paper sections in one multimodal LLM call and merges them into an existing LaTeX template. It is used to fill in Abstract, Methodology, Experiments, and Conclusion from the outline, figures, and experimental log.

**Install:**

```bash
npx degit https://github.com/Ar9av/PaperOrchestra/tree/main/skills/section-writing-agent ~/.claude/skills/section-writing-agent
```

## README

# Section Writing Agent (Step 4)

Faithful implementation of the Section Writing Agent from PaperOrchestra
(Song et al., 2026, arXiv:2604.05018, §4 Step 4, App. F.1 pp. 47–49).

**Cost: ONE LLM call** (App. B: "Section Writing Agent (1 call): A single,
comprehensive multimodal call to draft and compile the complete LaTeX
manuscript"). Do NOT split this into per-section calls — the paper
explicitly designs it as one comprehensive call so the model can maintain
global coherence across sections.

## Inputs

- `workspace/outline.json` — the master plan
- `workspace/inputs/idea.md` — technical details
- `workspace/inputs/experimental_log.md` — raw data for tables and qualitative analysis
- `workspace/drafts/intro_relwork.tex` — the template **with Intro + Related
  Work already filled in by Step 3**. This is your starting point. The
  preamble, package list, style, and the two pre-filled sections must be
  preserved verbatim.
- `workspace/citation_pool.json` — the citation map (`{key, title, abstract}`
  for each verified paper)
- `workspace/refs.bib` — the BibTeX file
- `workspace/inputs/conference_guidelines.md` — formatting rules
- `workspace/figures/` — the actual PNG files from Step 2 (used as
  multimodal vision input!)
- `workspace/figures/captions.json` — caption text per figure_id
- `workspace/tex_profile.json` — TeX package availability flags (written by
  `check_tex_packages.py` at Step 0). **Read this before generating any
  LaTeX.** It tells you which packages are installed so you select the right
  cross-reference pattern, font packages, etc. before you write — not after
  you try to compile.

## Output

- `workspace/drafts/paper.tex` — the complete LaTeX paper, with all sections
  filled. The Step 5 Refinement Agent will iterate on this file.

## How to do it

### 0.5. Read tex_profile.json and select LaTeX patterns

Before composing the prompt, read `workspace/tex_profile.json` and apply
these rules to every LaTeX choice in the generated paper:

| Profile flag | True → use | False → use instead |
|---|---|---|
| `use_cleveref` | `\cref{fig:X}`, `\cref{tab:Y}` | `Figure~\ref{fig:X}`, `Table~\ref{tab:Y}` |
| `use_nicefrac` | `\nicefrac{a}{b}` | `$a/b$` |
| `use_microtype` | `\usepackage{microtype}` | omit the line |
| `use_t1_fontenc` | `\usepackage[T1]{fontenc}` | omit the line |

If `tex_profile.json` does not exist (old workspace), default to the safe
fallback column (no cleveref, no nicefrac, no microtype, no T1 fontenc).

### 1. Pre-extract metrics from the experimental log

Run the deterministic helper:

```bash
python skills/section-writing-agent/scripts/extract_metrics.py \
    --log workspace/inputs/experimental_log.md \
    --out workspace/metrics.json
```

This parses the `## 2. Raw Numeric Data` section's markdown tables into
structured JSON. The Section Writing Agent uses this to construct LaTeX
booktabs tables without re-deriving values from raw text. Read
`references/latex-table-patterns.md` for the booktabs conventions.

### 2. Compose the prompt and make ONE multimodal call

Load `references/prompt.md` (verbatim Section Writing Agent prompt from App.
F.1). Prepend the Anti-Leakage Prompt from
`../paper-orchestra/references/anti-leakage-prompt.md`.

The user message contains:

- `outline.json` — full content
- `idea.md` — full content
- `experimental_log.md` — full content (tables AND prose)
- `intro_relwork.tex` — full content (this becomes `template.tex` for the prompt)
- `citation_pool.json` — full content (becomes `citation_map.json`)
- `conference_guidelines.md` — full content
- `figures_list` — array of `{figure_id, filename, caption}` from
  `captions.json` and the file listing
- **The actual figure PNGs** as multimodal image inputs, so the model can
  visually inspect them and write accurate descriptions / refer to them
  correctly in the prose.

If your host LLM has no vision input, fall back to text-only mode: pass the
captions in `captions.json` as descriptions and tell the agent it cannot see
the images directly. Quality drops noticeably (the paper notes that visual
grounding measurably improves figure-text alignment), but the pipeline
still completes.

### 3. Save the output

The agent's response is wrapped in `\`\`\`latex ... \`\`\`` fences. Extract
the LaTeX code and save to `workspace/drafts/paper.tex`.

### 4. Run the deterministic gates

```bash
# Orphan citation gate: every \cite{KEY} must exist in refs.bib
python skills/section-writing-agent/scripts/orphan_cite_gate.py \
    workspace/drafts/paper.tex workspace/refs.bib

# Latex sanity: matched braces, matched begin/end, no unescaped specials
python skills/section-writing-agent/scripts/latex_sanity.py \
    workspace/drafts/paper.tex

# Anti-leakage post-check: no author names, emails, affiliations
python skills/paper-orchestra/scripts/anti_leakage_check.py \
    workspace/drafts/paper.tex
```

If any gate fails, **re-prompt the writing call** with the gate's error
report appended to the user message and ask the agent to fix the specific
issues. Do NOT try to fix the gate violations by hand — the model needs to
see its own mistakes.

## Critical rules from the prompt

These are excerpted from `references/prompt.md` (App. F.1, pp. 47-49). The
host agent MUST honor them on the writing call:

### Existing-content preservation

- DO NOT modify the text, style, or content of sections that are already
  filled in `intro_relwork.tex`. Preserve Intro + Related Work verbatim.
- Keep the preamble (packages, document class, style) **exactly** as is.
- Come up with a good title if one is missing. Fill author names if missing
  (but the Anti-Leakage Prompt says not to invent real ones — use a
  placeholder like "Anonymous Authors" for double-blind).

### Data and tables

- Build LaTeX tables for the experimental results.
- Extract numeric values directly from `experimental_log.md`. **Do not
  hallucinate numbers** — use the exact values in the log.
- Use the `booktabs` package format: `\toprule`, `\midrule`, `\bottomrule`.
- All tables must appear before the Conclusion section, unless they are
  explicitly placed in an Appendix.

### Citations

- The `outline.json` provides citation_hints per subsection. For each hint,
  find the matching key in `citation_pool.json` (by title or content) and
  use that exact key in `\cite{...}`.
- **Use ONLY keys from `refs.bib`.** Inventing or guessing keys violates the
  Lit Review Agent's verified pool.
- **Read the abstract** from `citation_pool.json` for the papers you cite.
  Use the abstract context to write specific, accurate sentences about
  those works — not generic "[A, B] proposed methods for X".

### Writing content

- Write the missing sections following `outline.json`'s `section_plan`
  structure exactly. Hierarchy rule: if 4.1 exists, 4.2 must exist.
- Use formal mathematical equations, notations, and definitions where
  appropriate AND directly supported by `idea.md` or `experimental_log.md`.
  **Do not hallucinate math.** Do not use complex math just for the sake
  of it.
- Always provide detailed ablation studies and qualitative analysis of the
  experimental results: what worked, what does not, and why.
- Optional: discuss limitations and future work at the end.
- If you put anything in the Appendix, the Appendix section appears AFTER
  the References section, on a fresh new page.

### Figures and visual fidelity

- You are being given the actual image files of the figures. You MUST
  describe them faithfully and accurately. Do NOT hallucinate
  interpretations that contradict the visual evidence in the plots.
- Use ALL of the figures provided in `figures/`. Use the exact filenames
  including extensions (e.g., `.png`) in your `\includegraphics` commands.
- DO NOT merge or group multiple figures into one display.
- If the paper is in a 2-column format, prefer single-column figures
  (`\begin{figure}`) unless they are very wide.
- All figures must appear before the Conclusion section, unless explicitly
  in the Appendix.
- Refine the captions if necessary, but they are already provided in
  `captions.json` and should generally be used as-is.
- Do NOT include "Figure X" in the caption text — LaTeX handles numbering.

### Style

- Adopt the tone of a top-tier ML conference paper: dense, objective,
  technical.
- Match the indentation and spacing style of the original `template.tex`.
  Do not change the overall LaTeX style.

### LaTeX integrity

- The output must compile flawlessly out-of-the-box.
- All `\begin{X}` must match a `\end{X}` (e.g., `\begin{figure*}` must be
  closed with `\end{figure*}`, not `\end{figure}`).
- DO NOT change `\usepackage[capitalize]{cleveref}` to
  `\usepackage[capitalize]{cleverref}` — there is no `cleverref.sty`.
- **Always emit `\clearpage` immediately before `\bibliographystyle{...}`.**
  Without it, figures deferred by LaTeX's float algorithm will appear inside
  or after the References section — a hard-to-spot layout defect that only
  shows up in the compiled PDF. `\clearpage` forces all pending floats to be
  output before the bibliography starts. See
  `references/latex-table-patterns.md` for details.
- **Cross-references**: prefer `Figure~\ref{fig:X}` and `Table~\ref{tab:Y}`
  over bare `\ref{fig:X}`. This is necessary when `cleveref` is unavailable
  and produces readable prose in all cases. Use `\cref{...}` only when
  `cleveref.sty` is confirmed present.

### Output format

- Wrap the full updated `template.tex` in `\`\`\`latex ... \`\`\``.
- The previously empty sections should now be filled.
- Previously filled sections (Intro, Related Work) should remain mostly
  untouched; only adjust for consistency purposes.

## Resources

- `references/prompt.md` — verbatim Section Writing Agent prompt from App. F.1
- `references/latex-table-patterns.md` — booktabs rules + table-from-log examples
- `references/figure-integration.md` — `\includegraphics`, 2-column handling, placement
- `scripts/extract_metrics.py` — markdown tables in experimental_log → JSON
- `scripts/latex_sanity.py` — unmatched braces, env mismatches, specials
- `scripts/orphan_cite_gate.py` — every `\cite{KEY}` exists in refs.bib