Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Decompose research ideas into atomic, self-contained concepts with bidirectional math-code mapping.
Install Atomic Decomposition
$ npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install lingzhi227/agent-research-skills atomic-decomposition --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/atomic-decomposition .claude/skills/atomic-decomposition && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "atomic-decomposition" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/atomic-decomposition into .claude/skills/atomic-decomposition/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "atomic-decomposition", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/lingzhi227/agent-research-skills/tree/main/skills/atomic-decompositionType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install lingzhi227/agent-research-skills atomic-decomposition --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/atomic-decomposition .agents/skills/atomic-decomposition && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "atomic-decomposition" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/atomic-decomposition into .agents/skills/atomic-decomposition/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "atomic-decomposition", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install lingzhi227/agent-research-skills atomic-decomposition --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/atomic-decomposition .cursor/skills/atomic-decomposition && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "atomic-decomposition" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/atomic-decomposition into .cursor/skills/atomic-decomposition/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "atomic-decomposition", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/lingzhi227/agent-research-skills.git --path skills/atomic-decomposition--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install lingzhi227/agent-research-skills atomic-decomposition --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/atomic-decomposition .gemini/skills/atomic-decomposition && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "atomic-decomposition" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/atomic-decomposition into .gemini/skills/atomic-decomposition/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "atomic-decomposition", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install lingzhi227/agent-research-skills atomic-decompositionInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/atomic-decomposition .github/skills/atomic-decomposition && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "atomic-decomposition" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/atomic-decomposition into .github/skills/atomic-decomposition/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "atomic-decomposition", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install lingzhi227/agent-research-skills atomic-decomposition --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/lingzhi227/agent-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/atomic-decomposition .opencode/skills/atomic-decomposition && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "atomic-decomposition" agent skill from https://github.com/lingzhi227/agent-research-skills/tree/main/skills/atomic-decomposition into .opencode/skills/atomic-decomposition/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "atomic-decomposition", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
atomic-decomposition- GitHub stars
- 386
- Token cost
- ~712 tokens
- SKILL.md length
- 242 words
- Files
- 2 (incl. references)
- Skills in repo
- 31
- Repo updated
- First seen
- Licence
- None found
At a glance
Decompose research ideas into atomic, self-contained concepts with bidirectional math-code mapping.
- Works in 3 steps: Break Down into Atomic Definitions → For Each Atomic Definition → Compile Knowledge Base
- Complex system papers requiring formal grounding
- SKILL.md covers Input, References, Workflow (from AI-Researcher… and Rules, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Atomic Decomposition is an agent skill from lingzhi227/agent-research-skills. Decompose research ideas into atomic, self-contained concepts with bidirectional math-code mapping. For each concept, extract the math formula from papers and find code implementations. Use for complex system papers requiring formal grounding.
Its SKILL.md is about 710 tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files, including reference files (for example `references/decomposition-prompts.md`).
It sits in Research & Science, covering Hypothesis generation. The repository describes itself as: Skills for Claude Code — deep-research: systematic academic literature review.
When your agent uses it
- Complex system papers requiring formal grounding
- Tasks that involve Hypothesis generation
Example prompts
- “/atomic-decomposition”
Workflow steps
3 steps, taken from the step headings in SKILL.md.
- Break Down into Atomic Definitions
- For Each Atomic Definition
- Compile Knowledge Base
What it can do on your machine
Read from SKILL.md and the folder at commit 9e6c085. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are json).
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Atomic Decomposition loads about 712 tokens when it runs, and up to ~1.9k if it reads all its reference files. Until then it costs about 66 tokens; SKILL.md has 242 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 242 words (~712 tokens).
“Decompose research ideas into atomic concepts with math formula <-> code implementation mapping.”
- name
- atomic-decomposition
- argument-hint
- idea-or-paper
Files
SKILL.md and 1 other file (references) in skills/atomic-decomposition of lingzhi227/agent-research-skills.
- SKILL.md
- references/decomposition-prompts.md
Open the folder on GitHubat commit 9e6c085
Compare with similar skills
Atomic Decomposition next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Atomic Decomposition this skilllingzhi227/agent-research-skills | 386 | — | ~712 | Automated safety check: Pass | None | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Hypothesis GenerationK-Dense-AI/claude-scientific-writer | 2.4k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | |
| Good QuestionRimagination/good-question | 305 | 1 repos | ~4.3k | Automated safety check: Pass | MIT | |
| High Stakes Analytics Decision Lablimingrui679-design/high-stakes-analytics-decision-lab | 1k | — | ~2.2k | Automated safety check: Pass | MIT |
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Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Hypothesis Generation
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Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready…
Good Question
Rimagination/good-question
A skill your agent uses when a researcher is choosing, framing, refining, or stress-testing a research question, hypothesis, thesis topic, project idea, grant direction, paper angle, or stalled…
High Stakes Analytics Decision Lab
limingrui679-design/high-stakes-analytics-decision-lab
Build or review source-backed descriptive, diagnostic, predictive, and prescriptive analysis for consequential decisions.
Claim-Driven Experiment Planner
zjYao36/Auto-Research-Refine
Turns a refined research proposal into a claim-to-evidence-to-run-order roadmap instead of a sprawling benchmark wishlist.
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Related
Categories
Questions about Atomic Decomposition
What does Atomic Decomposition do?
Decompose research ideas into atomic, self-contained concepts with bidirectional math-code mapping. Atomic Decomposition is an agent skill from lingzhi227/agent-research-skills. Decompose research ideas into atomic, self-contained concepts with bidirectional math-code mapping.
When should I use Atomic Decomposition?
Atomic Decomposition fits situations like: complex system papers requiring formal grounding; tasks that involve Hypothesis generation.
How do I install Atomic Decomposition in Claude Code?
Run `npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a claude-code`. Or copy the skill folder (skills/atomic-decomposition in lingzhi227/agent-research-skills) into .claude/skills/atomic-decomposition in your project. Claude Code loads it when a task matches its description.
How do I install Atomic Decomposition in Codex?
Run `npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a codex`. Or copy the skill folder (skills/atomic-decomposition in lingzhi227/agent-research-skills) into .agents/skills/atomic-decomposition in your project. Codex loads it when a task matches its description.
Can I use Atomic Decomposition in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lingzhi227/agent-research-skills --skill atomic-decomposition -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/atomic-decomposition, .gemini/skills/atomic-decomposition, .github/skills/atomic-decomposition and .opencode/skills/atomic-decomposition in your project.
What does Atomic Decomposition need to run?
SKILL.md names no scripts, command-line tools or credentials: Atomic Decomposition is instructions for the agent only.
Does Atomic Decomposition access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is Atomic Decomposition safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Atomic Decomposition use?
No licence was found for Atomic Decomposition or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Atomic Decomposition use?
About 712 tokens (SKILL.md is roughly 2.8k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 1.2k tokens, read only when the agent opens those files.
What are the alternatives to Atomic Decomposition?
Skills that share tags, products or a category with Atomic Decomposition: Hypothesis Generation (spacering-net/codeg, 3.9k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars), Hypothesis Generation (K-Dense-AI/claude-scientific-writer, 2.4k stars) and Good Question (Rimagination/good-question, 305 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Atomic Decomposition?
lingzhi227 (a GitHub user) maintains it in lingzhi227/agent-research-skills, which has 386 GitHub stars. The repository holds 31 skills in this directory. The repository was last updated on February 27, 2026.
Source: lingzhi227/agent-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.