research-paper-writing

Research Paper Writing Pipeline

End-to-end pipeline for producing publication-ready ML/AI research papers targeting NeurIPS, ICML, ICLR, ACL, AAAI, and COLM. This skill covers the full research lifecycle: experiment design, execution, monitoring, analysis, paper writing, review, revision, and submission.

This is not a linear pipeline — it is an iterative loop. Results trigger new experiments. Reviews trigger new analysis. The agent must handle these feedback loops.

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┌─────────────────────────────────────────────────────────────┐
│                    RESEARCH PAPER PIPELINE                  │
│                                                             │
│  Phase 0: Project Setup ──► Phase 1: Literature Review      │
│       │                          │                          │
│       ▼                          ▼                          │
│  Phase 2: Experiment     Phase 5: Paper Drafting ◄──┐      │
│       Design                     │                   │      │
│       │                          ▼                   │      │
│       ▼                    Phase 6: Self-Review      │      │
│  Phase 3: Execution &           & Revision ──────────┘      │
│       Monitoring                 │                          │
│       │                          ▼                          │
│       ▼                    Phase 7: Submission               │
│  Phase 4: Analysis ─────► (feeds back to Phase 2 or 5)     │
│                                                             │
└─────────────────────────────────────────────────────────────┘

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When To Use This Skill

Use this skill when:

• Starting a new research paper from an existing codebase or idea
• Designing and running experiments to support paper claims
• Writing or revising any section of a research paper
• Preparing for submission to a specific conference or workshop
• Responding to reviews with additional experiments or revisions
• Converting a paper between conference formats
• Writing non-empirical papers — theory, survey, benchmark, or position papers (see [Paper Types Beyond Empirical ML](#paper-types-beyond-empirical-ml))
• Designing human evaluations for NLP, HCI, or alignment research
• Preparing post-acceptance deliverables — posters, talks, code releases

Core Philosophy

1. Be proactive. Deliver complete drafts, not questions. Scientists are busy — produce something concrete they can react to, then iterate.
2. Never hallucinate citations. AI-generated citations have ~40% error rate. Always fetch programmatically. Mark unverifiable citations as [CITATION NEEDED].
3. Paper is a story, not a collection of experiments. Every paper needs one clear contribution stated in a single sentence. If you can't do that, the paper isn't ready.
4. Experiments serve claims. Every experiment must explicitly state which claim it supports. Never run experiments that don't connect to the paper's narrative.
5. Commit early, commit often. Every completed experiment batch, every paper draft update — commit with descriptive messages. Git log is the experiment history.

Proactivity and Collaboration

Default: Be proactive. Draft first, ask with the draft.

| Confidence Level | Action | |-----------------|--------| | High (clear repo, obvious contribution) | Write full draft, deliver, iterate on feedback | | Medium (some ambiguity) | Write draft with flagged uncertainties, continue | | Low (major unknowns) | Ask 1-2 targeted questions via clarify, then draft |

| Section | Draft Autonomously? | Flag With Draft | |---------|-------------------|-----------------| | Abstract | Yes | "Framed contribution as X — adjust if needed" | | Introduction | Yes | "Emphasized problem Y — correct if wrong" | | Methods | Yes | "Included details A, B, C — add missing pieces" | | Experiments | Yes | "Highlighted results 1, 2, 3 — reorder if needed" | | Related Work | Yes | "Cited papers X, Y, Z — add any I missed" |

Block for input only when: target venue unclear, multiple contradictory framings, results seem incomplete, explicit request to review first.

Phase 0: Project Setup

Goal: Establish the workspace, understand existing work, identify the contribution.

Step 0.1: Explore the Repository

# Understand project structure
ls -la
find . -name "*.py" | head -30
find . -name "*.md" -o -name "*.txt" | xargs grep -l -i "result\|conclusion\|finding"

Look for:

• README.md — project overview and claims
• results/, outputs/, experiments/ — existing findings
• configs/ — experimental settings
• .bib files — existing citations
• Draft documents or notes

Step 0.2: Organize the Workspace

Establish a consistent workspace structure:

workspace/
  paper/               # LaTeX source, figures, compiled PDFs
  experiments/         # Experiment runner scripts
  code/                # Core method implementation
  results/             # Raw experiment results (auto-generated)
  tasks/               # Task/benchmark definitions
  human_eval/          # Human evaluation materials (if needed)

Step 0.3: Set Up Version Control

git init  # if not already
git remote add origin <repo-url>
git checkout -b paper-draft  # or main

Git discipline: Every completed experiment batch gets committed with a descriptive message. Example:

Add Monte Carlo constrained results (5 runs, Sonnet 4.6, policy memo task)
Add Haiku baseline comparison: autoreason vs refinement baselines at cheap model tier

Step 0.4: Identify the Contribution

Before writing anything, articulate:

• The What: What is the single thing this paper contributes?
• The Why: What evidence supports it?
• The So What: Why should readers care?

Propose to the scientist: "Based on my understanding, the main contribution is: [one sentence]. The key results show [Y]. Is this the framing you want?"

Step 0.5: Create a TODO List

Use the todo tool to create a structured project plan:

Research Paper TODO:
- [ ] Define one-sentence contribution
- [ ] Literature review (related work + baselines)
- [ ] Design core experiments
- [ ] Run experiments
- [ ] Analyze results
- [ ] Write first draft
- [ ] Self-review (simulate reviewers)
- [ ] Revise based on review
- [ ] Submission prep

Update this throughout the project. It serves as the persistent state across sessions.

Step 0.6: Estimate Compute Budget

Before running experiments, estimate total cost and time:

Compute Budget Checklist:
- [ ] API costs: (model price per token) × (estimated tokens per run) × (number of runs)
- [ ] GPU hours: (time per experiment) × (number of experiments) × (number of seeds)
- [ ] Human evaluation costs: (annotators) × (hours) × (hourly rate)
- [ ] Total budget ceiling and contingency (add 30-50% for reruns)

Track actual spend as experiments run:

# Simple cost tracker pattern
import json, os
from datetime import datetime

COST_LOG = "results/cost_log.jsonl"

def log_cost(experiment: str, model: str, input_tokens: int, output_tokens: int, cost_usd: float):
    entry = {
        "timestamp": datetime.now().isoformat(),
        "experiment": experiment,
        "model": model,
        "input_tokens": input_tokens,
        "output_tokens": output_tokens,
        "cost_usd": cost_usd,
    }
    with open(COST_LOG, "a") as f:
        f.write(json.dumps(entry) + "\n")

When budget is tight: Run pilot experiments (1-2 seeds, subset of tasks) before committing to full sweeps. Use cheaper models for debugging pipelines, then switch to target models for final runs.

Step 0.7: Multi-Author Coordination

Most papers have 3-10 authors. Establish workflows early:

| Workflow | Tool | When to Use | |----------|------|-------------| | Overleaf | Browser-based | Multiple authors editing simultaneously, no git experience | | **