# Paper Creator

> Scientific paper writing in LaTeX -- full pipeline from structure to compiled PDF. TDD-driven: every section is compiled and verified before moving to the next. Covers project scaffolding, citation management (OpenAlex to BibTeX), per-section academic writing with self-reflection, figure/table inclusion, LaTeX compilation, and comprehensive verification. Triggers on: 'write a paper', 'create a paper', 'academic paper about', 'scientific paper', 'LaTeX paper', 'write up results as a paper', 'draft a paper on', 'research paper about', any request to produce a formal academic/scientific paper in LaTeX. Assumes research findings, data, and/or figures already exist or will be provided -- this skill handles the WRITING, not the experimentation.

- Skill: `kortix-ai/paper-creator` (Agent Skill, multi-file: 5 files)
- Install (CLI): `npx skillmds@latest add kortix-ai/paper-creator`
- Raw SKILL.md: https://api.skillmd.com/api/skills/kortix-ai/paper-creator/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: DevOps & Infra
- Author: kortix-ai (https://skillmd.com/u/kortix-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/kortix-ai/paper-creator

---


# Scientific Paper Creator

Write publication-quality scientific papers in LaTeX with a **test-driven workflow**: every section is compiled and verified before moving to the next. The paper is never in a broken state.

## Bundled Resources

This skill includes ready-to-use scripts and templates. Paths are relative to the skill directory (find it via `glob("**/KORTIX-paper-creator/")`):

| Resource | Path | Purpose |
|----------|------|---------|
| **LaTeX template** | `assets/template.tex` | Minimal IMRaD template -- copy to `main.tex` |
| **BibTeX generator** | `scripts/openalex_to_bibtex.py` | Convert OpenAlex API JSON to `.bib` entries |
| **Compiler** | `scripts/compile.sh` | `pdflatex + bibtex` pipeline with error reporting |
| **Verifier** | `scripts/verify.sh` | TDD verification suite (12 checks) |

## The TDD Rule

**After writing every section:**

```
1. WRITE section → sections/{name}.tex
2. COMPILE: bash compile.sh paper/{slug}/main.tex
3. VERIFY:  bash verify.sh paper/{slug}/
4. If FAIL → FIX → go to 2
5. If PASS → move to next section
```

The paper must compile and pass verification at every step. Never batch errors. Never skip verification. This is non-negotiable.

## Pipeline Overview

```
Phase 1: SCAFFOLD  →  Create project, copy template, initialize empty sections
                       Verify: compiles to valid (empty) PDF ✓

Phase 2: CITE      →  Search literature (OpenAlex), build references.bib
                       Verify: bibliography builds without errors ✓

Phase 3: WRITE     →  Per-section composition in writing order
                       Verify: compile + verify after EACH section ✓

Phase 4: POLISH    →  Self-reflection pass, strict verification, final build
                       Verify: verify.sh --strict passes with zero warnings ✓
```

## Filesystem Architecture

```
paper/{paper-slug}/
├── main.tex                    # Master file (\input sections)
├── references.bib              # BibTeX bibliography
├── sections/
│   ├── abstract.tex
│   ├── introduction.tex
│   ├── related-work.tex
│   ├── methods.tex
│   ├── results.tex
│   ├── discussion.tex
│   └── conclusion.tex
├── figures/                    # .pdf/.png figures (+ generation scripts)
├── data/                       # Supporting data, CSVs (optional)
└── build/                      # Compilation output
    └── main.pdf
```

## Phase 1: Scaffold

### 1a. Create project structure

```bash
SLUG="paper-slug-here"
mkdir -p "paper/$SLUG"/{sections,figures,data,build}
```

### 1b. Copy and adapt the template

```bash
SKILL_DIR=$(find . -path "*/KORTIX-paper-creator/assets/template.tex" -exec dirname {} \; | head -1 | sed 's|/assets||')
cp "$SKILL_DIR/assets/template.tex" "paper/$SLUG/main.tex"
```

Edit `main.tex`: set `\title{}`, `\author{}`, and adapt `\documentclass` if targeting a specific venue:

| Venue | Document class | Notes |
|-------|---------------|-------|
| General / arXiv | `\documentclass[11pt,a4paper]{article}` | Default in template |
| IEEE conference | `\documentclass[conference]{IEEEtran}` | Remove geometry package |
| ACM conference | `\documentclass[sigconf]{acmart}` | Remove geometry, use acmart bib style |
| Springer LNCS | `\documentclass{llncs}` | Remove geometry, use splncs04 bib style |

### 1c. Initialize section stubs

Create each section file with a section header and TODO marker:

```bash
for sec in abstract introduction related-work methods results discussion conclusion; do
    SECTION_TITLE=$(echo "$sec" | sed 's/-/ /g; s/\b\(.\)/\u\1/g')
    if [ "$sec" = "abstract" ]; then
        echo '\begin{abstract}' > "paper/$SLUG/sections/$sec.tex"
        echo "% TODO: Write abstract" >> "paper/$SLUG/sections/$sec.tex"
        echo '\end{abstract}' >> "paper/$SLUG/sections/$sec.tex"
    else
        echo "\\section{$SECTION_TITLE}" > "paper/$SLUG/sections/$sec.tex"
        echo "\\label{sec:$sec}" >> "paper/$SLUG/sections/$sec.tex"
        echo "% TODO: Write $sec" >> "paper/$SLUG/sections/$sec.tex"
    fi
done
```

### 1d. Initialize empty bibliography

```bash
echo "% References for $SLUG" > "paper/$SLUG/references.bib"
echo "% Generated by openalex_to_bibtex.py and manual entries" >> "paper/$SLUG/references.bib"
```

### 1e. VERIFY: First green state

```bash
bash "$SKILL_DIR/scripts/compile.sh" "paper/$SLUG/main.tex"
bash "$SKILL_DIR/scripts/verify.sh" "paper/$SLUG/"
```

The empty paper must compile cleanly. This is your baseline. Every subsequent change maintains this green state.

## Phase 2: Literature & Citations

### 2a. Search for papers

Load the `openalex-paper-search` skill for OpenAlex API reference. Search strategy:

```bash
# Seminal/highly-cited papers
curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&filter=cited_by_count:>50,type:article,has_abstract:true&sort=cited_by_count:desc&per_page=15&select=id,display_name,publication_year,cited_by_count,doi,authorships,abstract_inverted_index&mailto=agent@kortix.ai"

# Recent work (last 2-3 years)
curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&filter=publication_year:>2023,type:article&sort=publication_date:desc&per_page=15&mailto=agent@kortix.ai"

# Review/survey papers
curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&filter=type:review&sort=cited_by_count:desc&per_page=10&mailto=agent@kortix.ai"
```

### 2b. Generate BibTeX entries

Pipe OpenAlex results through the converter:

```bash
curl -s "https://api.openalex.org/works?search=YOUR+TOPIC&per_page=20&mailto=agent@kortix.ai" | \
    python3 "$SKILL_DIR/scripts/openalex_to_bibtex.py" >> "paper/$SLUG/references.bib"
```

For non-OpenAlex sources (web pages, books, reports), add manual BibTeX entries:

```bibtex
@misc{authorYYYYtitle,
  title = {Page Title},
  author = {Author Name},
  year = {2024},
  url = {https://example.com/page},
  note = {Accessed: 2024-01-15}
}

@book{authorYYYYbook,
  title = {Book Title},
  author = {First Author and Second Author},
  year = {2024},
  publisher = {Publisher Name},
  edition = {2nd}
}
```

### 2c. VERIFY: Bibliography builds

```bash
bash "$SKILL_DIR/scripts/compile.sh" "paper/$SLUG/main.tex"
bash "$SKILL_DIR/scripts/verify.sh" "paper/$SLUG/"
```

Check: zero BibTeX errors, all `.bib` entries parse correctly.

## Phase 3: Per-Section Writing

### Writing Order

Write sections in this order (each one builds on context from the previous):

1. **Abstract** (draft) -- establishes scope, will be revised last
2. **Introduction** -- context, problem, gap, contribution
3. **Methods** -- what you did and how
4. **Results** -- what you found
5. **Discussion** -- what it means, limitations
6. **Related Work** -- needs full paper context to position contribution
7. **Conclusion** -- recap, future work
8. **Abstract** (final) -- revise to match actual paper content

### The Writing Loop (for each section)

```
1. READ all previously written sections to build context
2. WRITE the section following the guidance below
3. COMPILE + VERIFY
4. SELF-REFLECT: re-read critically
   - Every factual claim has a \cite{}?
   - No filler words or empty hedging?
   - Logical flow between paragraphs?
   - Consistent with other sections?
   - Quantitative where possible?
5. REVISE if needed → COMPILE + VERIFY again
6. Section DONE → next
```

### Section-Specific Guidance

#### Abstract (150-300 words)

Structure: **Context** (1-2 sentences) → **Problem** → **Approach** → **Key results** (quantitative!) → **Implications**.

```latex
\begin{abstract}
[Context sentence setting the broad area.]
[Problem: what gap or challenge exists.]
[Approach: what this paper does -- "We propose/present/introduce..."]
[Results: key quantitative findings -- "Our method achieves X\% on Y, outperforming Z by N\%."]
[Implications: why it matters.]
\end{abstract}
```

Rules: No citations in abstract. No undefined acronyms. Every number must appear in the actual results.

#### Introduction

**Funnel structure:** broad context → specific problem → gap in existing work → your contribution → paper outline.

```latex
\section{Introduction}
\label{sec:introduction}

% Paragraph 1: Broad context (2-3 sentences)
% Paragraph 2: Narrow to specific problem
% Paragraph 3: What's been tried, what's missing (the gap)
% Paragraph 4: Your contribution -- be specific and concrete
%   "Our contributions are as follows:
%   \begin{itemize}
%     \item We propose...
%     \item We demonstrate...
%     \item We release...
%   \end{itemize}"
% Paragraph 5: Paper outline
%   "The remainder of this paper is organized as follows. \secref{sec:related-work} reviews..."
```

Rules: End with explicit contribution list. Every contribution claimed here must be backed by evidence in Results/Discussion.

#### Methods

**Reproducible detail.** Another researcher should be able to replicate your work from this section alone.

```latex
\section{Methods}
\label{sec:methods}

% Define notation before using it:
% "Let $\mathcal{D} = \{(x_i, y_i)\}_{i=1}^{N}$ denote the training set..."

% Algorithms as pseudocode:
% \begin{algorithm}[t]
%   \caption{Algorithm Name}
%   \label{alg:name}
%   \begin{algorithmic}[1]
%     \REQUIRE Input description
%     \ENSURE Output description
%     \STATE Step 1
%     \FOR{condition}
%       \STATE Step in loop
%     \ENDFOR
%     \RETURN result
%   \end{algorithmic}
% \end{algorithm}
```

Rules: Define all notation. Be precise about dimensions, loss functions, optimization details. Use consistent math notation throughout (define `\newcommand` macros in `main.tex` preamble).

#### Results

**Lead with the main finding.** Then support with details.

```latex
\section{Results}
\label{sec:results}

% Paragraph 1: Main result (the headline number)
% "Our method achieves X\% accuracy on Y benchmark, representing a Z\% improvement
%  over the previous state of the art~\citep{baseline2024}."

% Table with main results:
% \begin{table}[t]
%   \centering
%   \caption{Main results on [benchmark]. Bold = best, underline = second best.}
%   \label{tab:main-results}
%   \begin{tabular}{lcc}
%     \toprule
%     Method & Metric 1 & Metric 2 \\
%     \midrule
%     Baseline A~\citep{ref} & 82.3 & 91.1 \\
%     Baseline B~\citep{ref} & 84.7 & 92.4 \\
%     \textbf{Ours} & \textbf{87.2} & \textbf{94.1} \\
%     \bottomrule
%   \end{tabular}
% \end{table}

% Subsequent paragraphs: ablation studies, analysis, per-dataset breakdown
% Every figure and table MUST be referenced: "As shown in \figref{fig:x}..."
```

Rules: Every figure/table referenced in text at least once. Report statistical significance or confidence intervals where applicable. No cherry-picking -- report all metrics, including where you don't win.

#### Discussion

**Interpretation, not repetition.** Don't restate results -- explain what they mean.

```latex
\section{Discussion}
\label{sec:discussion}

% Paragraph 1: Interpret main findings -- what do the results tell us?
% Paragraph 2: Compare with prior work -- how do results relate to existing literature?
% Paragraph 3: Limitations -- be honest and specific
%   "Our approach has several limitations. First, ... Second, ..."
% Paragraph 4: Broader implications -- what does this enable?
% Paragraph 5: Future work -- concrete directions, not vague hand-waving
```

Rules: Limitations must be genuine, not token gestures. Future work should be specific enough to be actionable.

#### Related Work

Written **after** Methods/Results/Discussion so you can precisely position your contribution against the literature.

```latex
\section{Related Work}
\label{sec:related-work}

% Organize THEMATICALLY, not chronologically:
% \subsection{Theme A}
% "Several works have addressed ... \citep{a,b,c}. Specifically, A does X, B does Y.
%  In contrast, our approach differs by Z."
%
% \subsection{Theme B}
% "Another line of work focuses on ... \citep{d,e,f}.
%  While these methods ..., they do not address ..., which is the focus of our work."
```

Rules: For each group of related work, explicitly state how your work differs. Don't just list papers -- synthesize and contrast. Every paper cited here should be in `references.bib`.

#### Conclusion

**No new information.** Brief recap of contribution and results, then future directions.

```latex
\section{Conclusion}
\label{sec:conclusion}

% Paragraph 1: What we did and what we found (3-4 sentences max)
% "In this paper, we presented [method] for [problem].
%  Our approach [key insight]. Experiments on [benchmarks] demonstrate [main result]."
%
% Paragraph 2: Future directions (2-3 sentences)
% "In future work, we plan to explore ... and extend our approach to ..."
```

Rules: Claims here must match what's in Results. Don't overclaim. 0.5-1 page max.

### LaTeX Conventions

Enforce these throughout all sections:

**Cross-references** (defined as macros in template):
```latex
\figref{fig:architecture}    % → "Figure 1"  (via cleveref)
\tabref{tab:main-results}    % → "Table 2"
\eqnref{eq:loss}             % → "Equation 3"
\secref{sec:methods}         % → "Section 4"
```

**Citations:**
```latex
\citet{smith2024}            % → "Smith et al. (2024)"     (textual -- subject of sentence)
\citep{smith2024}            % → "(Smith et al., 2024)"    (parenthetical)
\citep{smith2024,jones2023}  % → "(Smith et al., 2024; Jones et al., 2023)"
```

Use `\citet` when the author is the grammatical subject: "**\citet{smith2024} showed** that...". Use `\citep` for parenthetical: "Recent work has shown significant gains **\citep{smith2024}**."

**Figures:**
```latex
\begin{figure}[t]
  \centering
  \includegraphics[width=\linewidth]{figure-name}
  \caption{Descriptive caption. Best viewed in color.}
  \label{fig:figure-name}
\end{figure}
```

**Tables:**
```latex
\begin{table}[t]
  \centering
  \caption{Caption ABOVE the table (convention).}
  \label{tab:table-name}
  \begin{tabular}{lcc}
    \toprule
    Column 1 & Column 2 & Column 3 \\
    \midrule
    Row 1 & data & data \\
    Row 2 & data & data \\
    \bottomrule
  \end{tabular}
\end{table}
```

**Math notation:** Define reusable macros in the preamble of `main.tex`:
```latex
\newcommand{\loss}{\mathcal{L}}
\newcommand{\model}{\mathcal{M}}
\newcommand{\dataset}{\mathcal{D}}
\newcommand{\R}{\mathbb{R}}
\newcommand{\E}{\mathbb{E}}
\newcommand{\argmin}{\operatorname{argmin}}
```

## Phase 4: Polish & Final Verification

### 4a. Self-Reflection Pass

After all sections are written, re-read the entire paper and check:

1. **Consistency:** Same terminology throughout? Abstract claims match Results numbers?
2. **Redundancy:** Any paragraph repeated across sections? Cut ruthlessly.
3. **Flow:** Smooth transitions between sections? Each section starts by connecting to the previous?
4. **Claims:** Every claim in Intro/Abstract backed by evidence in Results?
5. **Notation:** Math notation consistent? All symbols defined before first use?

### 4b. Strict Verification

```bash
bash "$SKILL_DIR/scripts/verify.sh" "paper/$SLUG/" --strict
```

The `--strict` flag treats warnings as failures. All 12 checks must pass:

- [ ] PDF exists and is non-trivial size
- [ ] Zero LaTeX errors
- [ ] Zero undefined `\ref{}` references
- [ ] Zero undefined `\cite{}` citations
- [ ] Zero BibTeX errors
- [ ] Zero overfull boxes > 10pt
- [ ] All referenced figure files exist
- [ ] All sections have content (no empty stubs)
- [ ] All `.bib` entries cited at least once (no dead refs)
- [ ] Zero TODO/FIXME comments remaining
- [ ] Abstract word count 100-300
- [ ] All figures/tables referenced in text

### 4c. Final Build

```bash
bash "$SKILL_DIR/scripts/compile.sh" "paper/$SLUG/main.tex" --clean
```

The `--clean` flag removes auxiliary files, leaving only the PDF. Deliverable: `paper/{slug}/build/main.pdf`.

## Figure Generation

When the paper needs figures, generate them as PDF or high-res PNG and save to `figures/`. Keep the generation script alongside for reproducibility.

### matplotlib (recommended for most plots)

```python
import matplotlib.pyplot as plt
import matplotlib
matplotlib.rcParams.update({
    'font.size': 12,
    'font.family': 'serif',
    'figure.figsize': (6, 4),
    'figure.dpi': 150,
    'savefig.dpi': 300,
    'savefig.bbox': 'tight',
    'axes.grid': True,
    'grid.alpha': 0.3,
})

fig, ax = plt.subplots()
# ... plot data ...
ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.legend()
fig.savefig('paper/{slug}/figures/plot-name.pdf')
plt.close()
```

Rules:
- **Always save as PDF** for vector quality (PNG only for raster images like photos/heatmaps)
- Font size >= 10pt (readable when scaled to column width)
- Save the plotting script to `figures/plot_name.py` for reproducibility
- Use consistent color palettes across all figures
- Include axis labels, legends, and titles

### Diagrams and Architecture Figures

For architecture/flow diagrams, either:
- Generate with matplotlib/tikz and save as PDF
- Use `image-gen` tool and save to `figures/`
- Hand-draw in any tool and export as PDF/PNG

## LaTeX Troubleshooting

Common errors and fixes:

| Error | Cause | Fix |
|-------|-------|-----|
| `Missing $ inserted` | Math symbol outside math mode | Wrap in `$...$` |
| `Undefined control sequence` | Typo in command or missing package | Check spelling, add `\usepackage` |
| `File not found` | Wrong path in `\includegraphics` | Check `\graphicspath` and filename |
| `Citation undefined` | Key mismatch between `\cite` and `.bib` | Check exact key spelling |
| `Missing \begin{document}` | Error in preamble | Check for typos above `\begin{document}` |
| `Overfull \hbox` | Line too wide | Rephrase, add `\linebreak`, or use `\sloppy` locally |
| `Package clash` | Two packages conflict | Check compatibility, load order matters |

When compile fails: read the **first** error in the log (subsequent errors often cascade from the first). Fix it, recompile. Don't try to fix multiple errors at once.

## Scientific Writing Standards

Quick-reference checklist for quality prose:

- **Active voice:** "We propose X" not "X is proposed"
- **Strong verbs:** "achieves" not "is able to achieve", "reduces" not "leads to a reduction in"
- **Quantitative:** "improves by 12%" not "significantly improves"
- **Define before use:** Every acronym, symbol, and technical term defined on first use
- **Parallel structure:** Lists and comparisons use the same grammatical form
- **No orphan pronouns:** "This approach" not "This" alone at the start of a sentence
- **Hedging (appropriate):** "suggests" / "indicates" for uncertain claims; "demonstrates" / "establishes" for proven ones
- **Person:** "We" for authors' actions; passive voice sparingly for general facts; never "I" in multi-author papers
- **Tense:** Present for established facts and paper structure ("Section 3 presents..."); past for what you did ("We trained the model on...")
- **Citations as nouns:** "\citet{smith2024} showed..." (not "It was shown in \citep{smith2024}...")