Back to Hermes Agent

Phase 5: Paper Drafting (full procedure)

skills/research/research-paper-writing/references/phase5-paper-drafting.md

2026.8.1331.1 KB
Original Source

Phase 5: Paper Drafting (full procedure)

Goal: Write a complete, publication-ready paper.

Context Management for Large Projects

A paper project with 50+ experiment files, multiple result directories, and extensive literature notes can easily exceed the agent's context window. Manage this proactively:

What to load into context per drafting task:

Drafting TaskLoad Into ContextDo NOT Load
Writing Introductionexperiment_log.md, contribution statement, 5-10 most relevant paper abstractsRaw result JSONs, full experiment scripts, all literature notes
Writing MethodsExperiment configs, pseudocode, architecture descriptionRaw logs, results from other experiments
Writing Resultsexperiment_log.md, result summary tables, figure listFull analysis scripts, intermediate data
Writing Related WorkOrganized citation notes (Step 1.4 output), .bib fileExperiment files, raw PDFs
Revision passFull paper draft, specific reviewer concernsEverything else

Principles:

  • experiment_log.md is the primary context bridge — it summarizes everything needed for writing without loading raw data files (see Step 4.6)
  • Load one section's context at a time when delegating. A sub-agent drafting Methods doesn't need the literature review notes.
  • Summarize, don't include raw files. For a 200-line result JSON, load a 10-line summary table. For a 50-page related paper, load the 5-sentence abstract + your 2-line note about its relevance.
  • For very large projects: Create a context/ directory with pre-compressed summaries:
    context/
      contribution.md          # 1 sentence
      experiment_summary.md    # Key results table (from experiment_log.md)
      literature_map.md        # Organized citation notes
      figure_inventory.md      # List of figures with descriptions
    

The Narrative Principle

The single most critical insight: Your paper is not a collection of experiments — it's a story with one clear contribution supported by evidence.

Every successful ML paper centers on what Neel Nanda calls "the narrative": a short, rigorous, evidence-based technical story with a takeaway readers care about.

Three Pillars (must be crystal clear by end of introduction):

PillarDescriptionTest
The What1-3 specific novel claimsCan you state them in one sentence?
The WhyRigorous empirical evidenceDo experiments distinguish your hypothesis from alternatives?
The So WhatWhy readers should careDoes this connect to a recognized community problem?

If you cannot state your contribution in one sentence, you don't yet have a paper.

The Sources Behind This Guidance

This skill synthesizes writing philosophy from researchers who have published extensively at top venues. The writing philosophy layer was originally compiled by Orchestra Research as the ml-paper-writing skill.

SourceKey ContributionLink
Neel Nanda (Google DeepMind)The Narrative Principle, What/Why/So What frameworkHow to Write ML Papers
Sebastian Farquhar (DeepMind)5-sentence abstract formulaHow to Write ML Papers
Gopen & Swan7 principles of reader expectationsScience of Scientific Writing
Zachary LiptonWord choice, eliminating hedgingHeuristics for Scientific Writing
Jacob Steinhardt (UC Berkeley)Precision, consistent terminologyWriting Tips
Ethan Perez (Anthropic)Micro-level clarity tipsEasy Paper Writing Tips
Andrej KarpathySingle contribution focusVarious lectures

For deeper dives into any of these, see:

Time Allocation

Spend approximately equal time on each of:

  1. The abstract
  2. The introduction
  3. The figures
  4. Everything else combined

Why? Most reviewers form judgments before reaching your methods. Readers encounter your paper as: title → abstract → introduction → figures → maybe the rest.

Writing Workflow

Paper Writing Checklist:
- [ ] Step 1: Define the one-sentence contribution
- [ ] Step 2: Draft Figure 1 (core idea or most compelling result)
- [ ] Step 3: Draft abstract (5-sentence formula)
- [ ] Step 4: Draft introduction (1-1.5 pages max)
- [ ] Step 5: Draft methods
- [ ] Step 6: Draft experiments & results
- [ ] Step 7: Draft related work
- [ ] Step 8: Draft conclusion & discussion
- [ ] Step 9: Draft limitations (REQUIRED by all venues)
- [ ] Step 10: Plan appendix (proofs, extra experiments, details)
- [ ] Step 11: Complete paper checklist
- [ ] Step 12: Final review

Two-Pass Refinement Pattern

When drafting with an AI agent, use a two-pass approach (proven effective in SakanaAI's AI-Scientist pipeline):

Pass 1 — Write + immediate refine per section: For each section, write a complete draft, then immediately refine it in the same context. This catches local issues (clarity, flow, completeness) while the section is fresh.

Pass 2 — Global refinement with full-paper context: After all sections are drafted, revisit each section with awareness of the complete paper. This catches cross-section issues: redundancy, inconsistent terminology, narrative flow, and gaps where one section promises something another doesn't deliver.

Second-pass refinement prompt (per section):
"Review the [SECTION] in the context of the complete paper.
- Does it fit with the rest of the paper? Are there redundancies with other sections?
- Is terminology consistent with Introduction and Methods?
- Can anything be cut without weakening the message?
- Does the narrative flow from the previous section and into the next?
Make minimal, targeted edits. Do not rewrite from scratch."

LaTeX Error Checklist

Append this checklist to every refinement prompt. These are the most common errors when LLMs write LaTeX:

LaTeX Quality Checklist (verify after every edit):
- [ ] No unenclosed math symbols ($ signs balanced)
- [ ] Only reference figures/tables that exist (\ref matches \label)
- [ ] No fabricated citations (\cite matches entries in .bib)
- [ ] Every \begin{env} has matching \end{env} (especially figure, table, algorithm)
- [ ] No HTML contamination (</end{figure}> instead of \end{figure})
- [ ] No unescaped underscores outside math mode (use \_ in text)
- [ ] No duplicate \label definitions
- [ ] No duplicate section headers
- [ ] Numbers in text match actual experimental results
- [ ] All figures have captions and labels
- [ ] No overly long lines that cause overfull hbox warnings

Step 5.0: Title

The title is the single most-read element of the paper. It determines whether anyone clicks through to the abstract.

Good titles:

  • State the contribution or finding: "Autoreason: When Iterative LLM Refinement Works and Why It Fails"
  • Highlight a surprising result: "Scaling Data-Constrained Language Models" (implies you can)
  • Name the method + what it does: "DPO: Direct Preference Optimization of Language Models"

Bad titles:

  • Too generic: "An Approach to Improving Language Model Outputs"
  • Too long: anything over ~15 words
  • Jargon-only: "Asymptotic Convergence of Iterative Stochastic Policy Refinement" (who is this for?)

Rules:

  • Include your method name if you have one (for citability)
  • Include 1-2 keywords reviewers will search for
  • Avoid colons unless both halves carry meaning
  • Test: would a reviewer know the domain and contribution from the title alone?

Step 5.1: Abstract (5-Sentence Formula)

From Sebastian Farquhar (DeepMind):

1. What you achieved: "We introduce...", "We prove...", "We demonstrate..."
2. Why this is hard and important
3. How you do it (with specialist keywords for discoverability)
4. What evidence you have
5. Your most remarkable number/result

Delete generic openings like "Large language models have achieved remarkable success..."

Step 5.2: Figure 1

Figure 1 is the second thing most readers look at (after abstract). Draft it before writing the introduction — it forces you to clarify the core idea.

Figure 1 TypeWhen to UseExample
Method diagramNew architecture or pipelineTikZ flowchart showing your system
Results teaserOne compelling result tells the whole storyBar chart: "Ours vs baselines" with clear gap
Problem illustrationThe problem is unintuitiveBefore/after showing failure mode you fix
Conceptual diagramAbstract contribution needs visual grounding2x2 matrix of method properties

Rules: Figure 1 must be understandable without reading any text. The caption alone should communicate the core idea. Use color purposefully — don't just decorate.

Step 5.3: Introduction (1-1.5 pages max)

Must include:

  • Clear problem statement
  • Brief approach overview
  • 2-4 bullet contribution list (max 1-2 lines each in two-column format)
  • Methods should start by page 2-3

Step 5.4: Methods

Enable reimplementation:

  • Conceptual outline or pseudocode
  • All hyperparameters listed
  • Architectural details sufficient for reproduction
  • Present final design decisions; ablations go in experiments

Step 5.5: Experiments & Results

For each experiment, explicitly state:

  • What claim it supports
  • How it connects to main contribution
  • What to observe: "the blue line shows X, which demonstrates Y"

Requirements:

  • Error bars with methodology (std dev vs std error)
  • Hyperparameter search ranges
  • Compute infrastructure (GPU type, total hours)
  • Seed-setting methods

Organize methodologically, not paper-by-paper. Cite generously — reviewers likely authored relevant papers.

Step 5.7: Limitations (REQUIRED)

All major conferences require this. Honesty helps:

  • Reviewers are instructed not to penalize honest limitation acknowledgment
  • Pre-empt criticisms by identifying weaknesses first
  • Explain why limitations don't undermine core claims

Step 5.8: Conclusion & Discussion

Conclusion (required, 0.5-1 page):

  • Restate the contribution in one sentence (different wording from abstract)
  • Summarize key findings (2-3 sentences, not a list)
  • Implications: what does this mean for the field?
  • Future work: 2-3 concrete next steps (not vague "we leave X for future work")

Discussion (optional, sometimes combined with conclusion):

  • Broader implications beyond immediate results
  • Connections to other subfields
  • Honest assessment of when the method does and doesn't work
  • Practical deployment considerations

Do NOT introduce new results or claims in the conclusion.

Step 5.9: Appendix Strategy

Appendices are unlimited at all major venues and are essential for reproducibility. Structure:

Appendix SectionWhat Goes Here
Proofs & DerivationsFull proofs too long for main text. Main text can state theorems with "proof in Appendix A."
Additional ExperimentsAblations, scaling curves, per-dataset breakdowns, hyperparameter sensitivity
Implementation DetailsFull hyperparameter tables, training details, hardware specs, random seeds
Dataset DocumentationData collection process, annotation guidelines, licensing, preprocessing
Prompts & TemplatesExact prompts used (for LLM-based methods), evaluation templates
Human EvaluationAnnotation interface screenshots, instructions given to annotators, IRB details
Additional FiguresPer-task breakdowns, trajectory visualizations, failure case examples

Rules:

  • The main paper must be self-contained — reviewers are not required to read appendices
  • Never put critical evidence only in the appendix
  • Cross-reference: "Full results in Table 5 (Appendix B)" not just "see appendix"
  • Use \appendix command, then \section{A: Proofs} etc.

Page Budget Management

When over the page limit:

Cut StrategySavesRisk
Move proofs to appendix0.5-2 pagesLow — standard practice
Condense related work0.5-1 pageMedium — may miss key citations
Combine tables with subfigures0.25-0.5 pageLow — often improves readability
Use \vspace{-Xpt} sparingly0.1-0.3 pageLow if subtle, high if obvious
Remove qualitative examples0.5-1 pageMedium — reviewers like examples
Reduce figure sizes0.25-0.5 pageHigh — figures must remain readable

Do NOT: reduce font size, change margins, remove required sections (limitations, broader impact), or use \small/\footnotesize for main text.

Step 5.10: Ethics & Broader Impact Statement

Most venues now require or strongly encourage an ethics/broader impact statement. This is not boilerplate — reviewers read it and can flag ethics concerns that trigger desk rejection.

What to include:

ComponentContentRequired By
Positive societal impactHow your work benefits societyNeurIPS, ICML
Potential negative impactMisuse risks, dual-use concerns, failure modesNeurIPS, ICML
Fairness & biasDoes your method/data have known biases?All venues (implicitly)
Environmental impactCompute carbon footprint for large-scale trainingICML, increasingly NeurIPS
PrivacyDoes your work use or enable processing of personal data?ACL, NeurIPS
LLM disclosureWas AI used in writing or experiments?ICLR (mandatory), ACL

Writing the statement:

latex
\section*{Broader Impact Statement}
% NeurIPS/ICML: after conclusion, does not count toward page limit

% 1. Positive applications (1-2 sentences)
This work enables [specific application] which may benefit [specific group].

% 2. Risks and mitigations (1-3 sentences, be specific)
[Method/model] could potentially be misused for [specific risk]. We mitigate
this by [specific mitigation, e.g., releasing only model weights above size X,
including safety filters, documenting failure modes].

% 3. Limitations of impact claims (1 sentence)
Our evaluation is limited to [specific domain]; broader deployment would
require [specific additional work].

Common mistakes:

  • Writing "we foresee no negative impacts" (almost never true — reviewers distrust this)
  • Being vague: "this could be misused" without specifying how
  • Ignoring compute costs for large-scale work
  • Forgetting to disclose LLM use at venues that require it

Compute carbon footprint (for training-heavy papers):

python
# Estimate using ML CO2 Impact tool methodology
gpu_hours = 1000  # total GPU hours
gpu_tdp_watts = 400  # e.g., A100 = 400W
pue = 1.1  # Power Usage Effectiveness (data center overhead)
carbon_intensity = 0.429  # kg CO2/kWh (US average; varies by region)

energy_kwh = (gpu_hours * gpu_tdp_watts * pue) / 1000
carbon_kg = energy_kwh * carbon_intensity
print(f"Energy: {energy_kwh:.0f} kWh, Carbon: {carbon_kg:.0f} kg CO2eq")

Step 5.11: Datasheets & Model Cards (If Applicable)

If your paper introduces a new dataset or releases a model, include structured documentation. Reviewers increasingly expect this, and NeurIPS Datasets & Benchmarks track requires it.

Datasheets for Datasets (Gebru et al., 2021) — include in appendix:

Dataset Documentation (Appendix):
- Motivation: Why was this dataset created? What task does it support?
- Composition: What are the instances? How many? What data types?
- Collection: How was data collected? What was the source?
- Preprocessing: What cleaning/filtering was applied?
- Distribution: How is the dataset distributed? Under what license?
- Maintenance: Who maintains it? How to report issues?
- Ethical considerations: Contains personal data? Consent obtained?
  Potential for harm? Known biases?

Model Cards (Mitchell et al., 2019) — include in appendix for model releases:

Model Card (Appendix):
- Model details: Architecture, training data, training procedure
- Intended use: Primary use cases, out-of-scope uses
- Metrics: Evaluation metrics and results on benchmarks
- Ethical considerations: Known biases, fairness evaluations
- Limitations: Known failure modes, domains where model underperforms

Writing Style

Sentence-level clarity (Gopen & Swan's 7 Principles):

PrincipleRule
Subject-verb proximityKeep subject and verb close
Stress positionPlace emphasis at sentence ends
Topic positionPut context first, new info after
Old before newFamiliar info → unfamiliar info
One unit, one functionEach paragraph makes one point
Action in verbUse verbs, not nominalizations
Context before newSet stage before presenting

Word choice (Lipton, Steinhardt):

  • Be specific: "accuracy" not "performance"
  • Eliminate hedging: drop "may" unless genuinely uncertain
  • Consistent terminology throughout
  • Avoid incremental vocabulary: "develop", not "combine"

Full writing guide with examples: See references/writing-guide.md

Using LaTeX Templates

Always copy the entire template directory first, then write within it.

Template Setup Checklist:
- [ ] Step 1: Copy entire template directory to new project
- [ ] Step 2: Verify template compiles as-is (before any changes)
- [ ] Step 3: Read the template's example content to understand structure
- [ ] Step 4: Replace example content section by section
- [ ] Step 5: Use template macros (check preamble for \newcommand definitions)
- [ ] Step 6: Clean up template artifacts only at the end

Step 1: Copy the Full Template

bash
cp -r templates/neurips2025/ ~/papers/my-paper/
cd ~/papers/my-paper/
ls -la  # Should see: main.tex, neurips.sty, Makefile, etc.

Copy the ENTIRE directory, not just the .tex file. Templates include style files (.sty), bibliography styles (.bst), example content, and Makefiles.

Step 2: Verify Template Compiles First

Before making ANY changes:

bash
latexmk -pdf main.tex
# Or manual: pdflatex main.tex && bibtex main && pdflatex main.tex && pdflatex main.tex

If the unmodified template doesn't compile, fix that first (usually missing TeX packages — install via tlmgr install <package>).

Step 3: Keep Template Content as Reference

Don't immediately delete example content. Comment it out and use as formatting reference:

latex
% Template example (keep for reference):
% \begin{figure}[t]
%   \centering
%   \includegraphics[width=0.8\linewidth]{example-image}
%   \caption{Template shows caption style}
% \end{figure}

% Your actual figure:
\begin{figure}[t]
  \centering
  \includegraphics[width=0.8\linewidth]{your-figure.pdf}
  \caption{Your caption following the same style.}
\end{figure}

Step 4: Replace Content Section by Section

Work through systematically: title/authors → abstract → introduction → methods → experiments → related work → conclusion → references → appendix. Compile after each section.

Step 5: Use Template Macros

latex
\newcommand{\method}{YourMethodName}  % Consistent method naming
\newcommand{\eg}{e.g.,\xspace}        % Proper abbreviations
\newcommand{\ie}{i.e.,\xspace}

Template Pitfalls

PitfallProblemSolution
Copying only .tex fileMissing .sty, won't compileCopy entire directory
Modifying .sty filesBreaks conference formattingNever edit style files
Adding random packagesConflicts, breaks templateOnly add if necessary
Deleting template content earlyLose formatting referenceKeep as comments until done
Not compiling frequentlyErrors accumulateCompile after each section
Raster PNGs for figuresBlurry in paperAlways use vector PDF via savefig('fig.pdf')

Quick Template Reference

ConferenceMain FileStyle FilePage Limit
NeurIPS 2025main.texneurips.sty9 pages
ICML 2026example_paper.texicml2026.sty8 pages
ICLR 2026iclr2026_conference.texiclr2026_conference.sty9 pages
ACL 2025acl_latex.texacl.sty8 pages (long)
AAAI 2026aaai2026-unified-template.texaaai2026.sty7 pages
COLM 2025colm2025_conference.texcolm2025_conference.sty9 pages

Universal: Double-blind, references don't count, appendices unlimited, LaTeX required.

Templates in templates/ directory. See templates/README.md for compilation setup (VS Code, CLI, Overleaf, other IDEs).

Tables and Figures

Tables — use booktabs for professional formatting:

latex
\usepackage{booktabs}
\begin{tabular}{lcc}
\toprule
Method & Accuracy $\uparrow$ & Latency $\downarrow$ \\
\midrule
Baseline & 85.2 & 45ms \\
\textbf{Ours} & \textbf{92.1} & 38ms \\
\bottomrule
\end{tabular}

Rules:

  • Bold best value per metric
  • Include direction symbols ($\uparrow$ higher better, $\downarrow$ lower better)
  • Right-align numerical columns
  • Consistent decimal precision

Figures:

  • Vector graphics (PDF, EPS) for all plots and diagrams — plt.savefig('fig.pdf')
  • Raster (PNG 600 DPI) only for photographs
  • Colorblind-safe palettes (Okabe-Ito or Paul Tol)
  • Verify grayscale readability (8% of men have color vision deficiency)
  • No title inside figure — the caption serves this function
  • Self-contained captions — reader should understand without main text

Conference Resubmission

For converting between venues, see Phase 7 (Submission Preparation) — it covers the full conversion workflow, page-change table, and post-rejection guidance.

Professional LaTeX Preamble

Add these packages to any paper for professional quality. They are compatible with all major conference style files:

latex
% --- Professional Packages (add after conference style file) ---

% Typography
\usepackage{microtype}              % Microtypographic improvements (protrusion, expansion)
                                     % Makes text noticeably more polished — always include

% Tables
\usepackage{booktabs}               % Professional table rules (\toprule, \midrule, \bottomrule)
\usepackage{siunitx}                % Consistent number formatting, decimal alignment
                                     % Usage: \num{12345} → 12,345; \SI{3.5}{GHz} → 3.5 GHz
                                     % Table alignment: S column type for decimal-aligned numbers

% Figures
\usepackage{graphicx}               % Include graphics (\includegraphics)
\usepackage{subcaption}             % Subfigures with (a), (b), (c) labels
                                     % Usage: \begin{subfigure}{0.48\textwidth} ... \end{subfigure}

% Diagrams and Algorithms
\usepackage{tikz}                   % Programmable vector diagrams
\usetikzlibrary{arrows.meta, positioning, shapes.geometric, calc, fit, backgrounds}
\usepackage[ruled,vlined]{algorithm2e}  % Professional pseudocode
                                     % Alternative: \usepackage{algorithmicx} if template bundles it

% Cross-references
\usepackage{cleveref}               % Smart references: \cref{fig:x} → "Figure 1"
                                     % MUST be loaded AFTER hyperref
                                     % Handles: figures, tables, sections, equations, algorithms

% Math (usually included by conference .sty, but verify)
\usepackage{amsmath,amssymb}        % AMS math environments and symbols
\usepackage{mathtools}              % Extends amsmath (dcases, coloneqq, etc.)

% Colors (for figures and diagrams)
\usepackage{xcolor}                 % Color management
% Okabe-Ito colorblind-safe palette:
\definecolor{okblue}{HTML}{0072B2}
\definecolor{okorange}{HTML}{E69F00}
\definecolor{okgreen}{HTML}{009E73}
\definecolor{okred}{HTML}{D55E00}
\definecolor{okpurple}{HTML}{CC79A7}
\definecolor{okcyan}{HTML}{56B4E9}
\definecolor{okyellow}{HTML}{F0E442}

Notes:

  • microtype is the single highest-impact package for visual quality. It adjusts character spacing at a sub-pixel level. Always include it.
  • siunitx handles decimal alignment in tables via the S column type — eliminates manual spacing.
  • cleveref must be loaded after hyperref. Most conference .sty files load hyperref, so put cleveref last.
  • Check if the conference template already loads any of these (especially algorithm, amsmath, graphicx). Don't double-load.

siunitx Table Alignment

siunitx makes number-heavy tables significantly more readable:

latex
\begin{tabular}{l S[table-format=2.1] S[table-format=2.1] S[table-format=2.1]}
\toprule
Method & {Accuracy $\uparrow$} & {F1 $\uparrow$} & {Latency (ms) $\downarrow$} \\
\midrule
Baseline         & 85.2  & 83.7  & 45.3 \\
Ablation (no X)  & 87.1  & 85.4  & 42.1 \\
\textbf{Ours}    & \textbf{92.1} & \textbf{90.8} & \textbf{38.7} \\
\bottomrule
\end{tabular}

The S column type auto-aligns on the decimal point. Headers in {} escape the alignment.

Subfigures

Standard pattern for side-by-side figures:

latex
\begin{figure}[t]
  \centering
  \begin{subfigure}[b]{0.48\textwidth}
    \centering
    \includegraphics[width=\textwidth]{fig_results_a.pdf}
    \caption{Results on Dataset A.}
    \label{fig:results-a}
  \end{subfigure}
  \hfill
  \begin{subfigure}[b]{0.48\textwidth}
    \centering
    \includegraphics[width=\textwidth]{fig_results_b.pdf}
    \caption{Results on Dataset B.}
    \label{fig:results-b}
  \end{subfigure}
  \caption{Comparison of our method across two datasets. (a) shows the scaling
  behavior and (b) shows the ablation results. Both use 5 random seeds.}
  \label{fig:results}
\end{figure}

Use \cref{fig:results} → "Figure 1", \cref{fig:results-a} → "Figure 1a".

Pseudocode with algorithm2e

latex
\begin{algorithm}[t]
\caption{Iterative Refinement with Judge Panel}
\label{alg:method}
\KwIn{Task $T$, model $M$, judges $J_1 \ldots J_n$, convergence threshold $k$}
\KwOut{Final output $A^*$}
$A \gets M(T)$ \tcp*{Initial generation}
$\text{streak} \gets 0$\;
\While{$\text{streak} < k$}{
  $C \gets \text{Critic}(A, T)$ \tcp*{Identify weaknesses}
  $B \gets M(T, C)$ \tcp*{Revised version addressing critique}
  $AB \gets \text{Synthesize}(A, B)$ \tcp*{Merge best elements}
  \ForEach{judge $J_i$}{
    $\text{rank}_i \gets J_i(\text{shuffle}(A, B, AB))$ \tcp*{Blind ranking}
  }
  $\text{winner} \gets \text{BordaCount}(\text{ranks})$\;
  \eIf{$\text{winner} = A$}{
    $\text{streak} \gets \text{streak} + 1$\;
  }{
    $A \gets \text{winner}$; $\text{streak} \gets 0$\;
  }
}
\Return{$A$}\;
\end{algorithm}

TikZ Diagram Patterns

TikZ is the standard for method diagrams in ML papers. Common patterns:

Pipeline/Flow Diagram (most common in ML papers):

latex
\begin{figure}[t]
\centering
\begin{tikzpicture}[
  node distance=1.8cm,
  box/.style={rectangle, draw, rounded corners, minimum height=1cm, 
              minimum width=2cm, align=center, font=\small},
  arrow/.style={-{Stealth[length=3mm]}, thick},
]
  \node[box, fill=okcyan!20] (input) {Input\\$x$};
  \node[box, fill=okblue!20, right of=input] (encoder) {Encoder\\$f_\theta$};
  \node[box, fill=okgreen!20, right of=encoder] (latent) {Latent\\$z$};
  \node[box, fill=okorange!20, right of=latent] (decoder) {Decoder\\$g_\phi$};
  \node[box, fill=okred!20, right of=decoder] (output) {Output\\$\hat{x}$};
  
  \draw[arrow] (input) -- (encoder);
  \draw[arrow] (encoder) -- (latent);
  \draw[arrow] (latent) -- (decoder);
  \draw[arrow] (decoder) -- (output);
\end{tikzpicture}
\caption{Architecture overview. The encoder maps input $x$ to latent 
representation $z$, which the decoder reconstructs.}
\label{fig:architecture}
\end{figure}

Comparison/Matrix Diagram (for showing method variants):

latex
\begin{tikzpicture}[
  cell/.style={rectangle, draw, minimum width=2.5cm, minimum height=1cm, 
               align=center, font=\small},
  header/.style={cell, fill=gray!20, font=\small\bfseries},
]
  % Headers
  \node[header] at (0, 0) {Method};
  \node[header] at (3, 0) {Converges?};
  \node[header] at (6, 0) {Quality?};
  % Rows
  \node[cell] at (0, -1) {Single Pass};
  \node[cell, fill=okgreen!15] at (3, -1) {N/A};
  \node[cell, fill=okorange!15] at (6, -1) {Baseline};
  \node[cell] at (0, -2) {Critique+Revise};
  \node[cell, fill=okred!15] at (3, -2) {No};
  \node[cell, fill=okred!15] at (6, -2) {Degrades};
  \node[cell] at (0, -3) {Ours};
  \node[cell, fill=okgreen!15] at (3, -3) {Yes ($k$=2)};
  \node[cell, fill=okgreen!15] at (6, -3) {Improves};
\end{tikzpicture}

Iterative Loop Diagram (for methods with feedback):

latex
\begin{tikzpicture}[
  node distance=2cm,
  box/.style={rectangle, draw, rounded corners, minimum height=0.8cm, 
              minimum width=1.8cm, align=center, font=\small},
  arrow/.style={-{Stealth[length=3mm]}, thick},
  label/.style={font=\scriptsize, midway, above},
]
  \node[box, fill=okblue!20] (gen) {Generator};
  \node[box, fill=okred!20, right=2.5cm of gen] (critic) {Critic};
  \node[box, fill=okgreen!20, below=1.5cm of $(gen)!0.5!(critic)$] (judge) {Judge Panel};
  
  \draw[arrow] (gen) -- node[label] {output $A$} (critic);
  \draw[arrow] (critic) -- node[label, right] {critique $C$} (judge);
  \draw[arrow] (judge) -| node[label, left, pos=0.3] {winner} (gen);
\end{tikzpicture}

latexdiff for Revision Tracking

Essential for rebuttals — generates a marked-up PDF showing changes between versions:

bash
# Install
# macOS: brew install latexdiff (or comes with TeX Live)
# Linux: sudo apt install latexdiff

# Generate diff
latexdiff paper_v1.tex paper_v2.tex > paper_diff.tex
pdflatex paper_diff.tex

# For multi-file projects (with \input{} or \include{})
latexdiff --flatten paper_v1.tex paper_v2.tex > paper_diff.tex

This produces a PDF with deletions in red strikethrough and additions in blue — standard format for rebuttal supplements.

SciencePlots for matplotlib

Install and use for publication-quality plots:

bash
pip install SciencePlots
python
import matplotlib.pyplot as plt
import scienceplots  # registers styles

# Use science style (IEEE-like, clean)
with plt.style.context(['science', 'no-latex']):
    fig, ax = plt.subplots(figsize=(3.5, 2.5))  # Single-column width
    ax.plot(x, y, label='Ours', color='#0072B2')
    ax.plot(x, y2, label='Baseline', color='#D55E00', linestyle='--')
    ax.set_xlabel('Training Steps')
    ax.set_ylabel('Accuracy')
    ax.legend()
    fig.savefig('paper/fig_results.pdf', bbox_inches='tight')

# Available styles: 'science', 'ieee', 'nature', 'science+ieee'
# Add 'no-latex' if LaTeX is not installed on the machine generating plots

Standard figure sizes (two-column format):

  • Single column: figsize=(3.5, 2.5) — fits in one column
  • Double column: figsize=(7.0, 3.0) — spans both columns
  • Square: figsize=(3.5, 3.5) — for heatmaps, confusion matrices