auto-research

name	auto-research
disable-model-invocation	true
description	Generate a program.md for autonomous AI research experiments (Karpathy's autoresearch paradigm). Interviews user about codebase, metric, and constraints, then produces a tailored program for an AI agent to iterate autonomously.
allowed-tools	["Read","Write","Edit","Glob","Grep","Bash","Agent"]

AutoResearch: Generate Autonomous Research Programs

You are creating a program.md — a natural language program that instructs an AI agent to conduct autonomous research experiments. The generated document is not documentation; it is executable instructions that an AI agent will follow literally, running experiments in an infinite loop.

The Core Idea

The human writes a research plan (program.md). The AI agent executes the experiment loop. Code is the agent's operating target, not the human's. The human sleeps; the agent works.

How This Skill Works

Phase 1: Interview the User

Before generating anything, you need to understand the research context. Ask the user about these areas (adapt based on what they've already told you — skip questions they've answered):

1. Project Basics

• What is the project about? (e.g., "training a small LLM", "optimizing a recommender system")
• Where is the codebase? (directory path)
• What language/framework? (Python/PyTorch, etc.)

2. File Scope

• Which file(s) should the agent modify? (the "experiment surface")
• Which files are read-only? (fixed infrastructure — evaluation, data loading, etc.)
• Are there any files the agent should read for context but not modify?

3. Metric & Goal

• What is the primary metric? (e.g., val_bpb, accuracy, F1, loss, latency)
• Direction: lower is better, or higher is better?
• How is it measured? (which script/function, what command to run)
• How to extract the result from output? (grep pattern or similar)

4. Experiment Execution

• What command runs a single experiment? (e.g., uv run train.py, python train.py)
• How long does one experiment take? (time budget)
• What hardware constraints exist? (GPU memory, CPU-only, MPS, etc.)

5. Data & Environment

• What data does the project use? Where is it stored?
• Any one-time setup steps needed before experiments can run?
• Any dependencies or environment requirements?

6. Constraints & Preferences

• Can the agent install new packages?
• Any specific areas the agent should focus on or avoid?
• Any simplicity preferences? (complexity budget for improvements)

Phase 2: Explore the Codebase

After the interview, read the key files to understand:

• The project structure
• The current metric output format
• The evaluation mechanism
• What parameters/architecture choices are available to modify

Phase 3: Generate program.md

Read the template at references/program-template.md and fill it in based on the interview and codebase exploration. The template contains {{PLACEHOLDER}} markers — replace each one with content tailored to the user's project.

Key Principles for Generation

1. Preserve the original spirit: The generated program.md must retain ALL sections from the template. Never remove sections — only customize their content. The structure (Setup, Experimentation rules, Output format, Logging, Experiment loop, Timeout, Crashes, NEVER STOP) is sacred.

2. Be specific: Replace generic placeholders with actual file names, actual commands, actual grep patterns. The agent following this document should not need to guess anything.

3. Calibrate the noise threshold: Based on the metric and experiment duration, set an appropriate threshold for distinguishing real improvement from noise. Short runs with high variance need larger thresholds.

4. Right-size the experiment priority list: Suggest experiment directions that make sense for the specific domain. An LLM training project has different levers than a reinforcement learning project or an image classifier.

5. Adapt constraints to the environment: A Mac with MPS has different constraints than an H100. Adjust VRAM warnings, batch size advice, and timeout values accordingly.

6. Enforce non-interactive operations: The generated program.md must emphasize that all commands run unattended. The template includes a "Non-interactive principle" section — ensure the run command, git operations, and any project-specific commands are configured with non-interactive flags. If the user's workflow involves commands that might prompt for input, identify and document the non-interactive alternatives during the interview phase.

Phase 4: Review with User

Present the generated program.md to the user. Walk them through the key sections and confirm:

• Are the file scopes correct?
• Is the metric extraction right?
• Are the experiment priorities sensible?
• Is the time budget appropriate?

Make adjustments based on feedback.

Phase 5: Save and Advise

Save the program.md to the project directory. Advise the user on how to start:

To start autonomous research:
1. Open a new Claude Code / AI agent session in the project directory
2. Prompt: "Read program.md and let's start. Do the setup first."
3. Confirm the setup, then let the agent run
4. Check results.tsv when you return