Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
A skill your agent uses when the user wants guided reading, deep reading, or structured analysis of a single paper, starting from fuzzy keywords or a research question.
Install Paper Guided Reading
$ npx skills add ZimoLiao/scholaraio --skill paper-guided-reading -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install ZimoLiao/scholaraio paper-guided-reading --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/ZimoLiao/scholaraio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/paper-guided-reading .claude/skills/paper-guided-reading && 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 "paper-guided-reading" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/paper-guided-reading into .claude/skills/paper-guided-reading/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-guided-reading", 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/ZimoLiao/scholaraio/tree/main/.claude/skills/paper-guided-readingType 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 ZimoLiao/scholaraio --skill paper-guided-reading -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install ZimoLiao/scholaraio paper-guided-reading --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .agents/skills && cp -r skills-src/.claude/skills/paper-guided-reading .agents/skills/paper-guided-reading && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "paper-guided-reading" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/paper-guided-reading into .agents/skills/paper-guided-reading/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-guided-reading", 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 ZimoLiao/scholaraio --skill paper-guided-reading -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install ZimoLiao/scholaraio paper-guided-reading --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/.claude/skills/paper-guided-reading .cursor/skills/paper-guided-reading && 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 "paper-guided-reading" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/paper-guided-reading into .cursor/skills/paper-guided-reading/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-guided-reading", 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/ZimoLiao/scholaraio.git --path .claude/skills/paper-guided-reading--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 ZimoLiao/scholaraio --skill paper-guided-reading -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install ZimoLiao/scholaraio paper-guided-reading --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/.claude/skills/paper-guided-reading .gemini/skills/paper-guided-reading && 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 "paper-guided-reading" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/paper-guided-reading into .gemini/skills/paper-guided-reading/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-guided-reading", 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 ZimoLiao/scholaraio paper-guided-readingInstalls 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 ZimoLiao/scholaraio --skill paper-guided-reading -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .github/skills && cp -r skills-src/.claude/skills/paper-guided-reading .github/skills/paper-guided-reading && 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 "paper-guided-reading" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/paper-guided-reading into .github/skills/paper-guided-reading/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-guided-reading", 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 ZimoLiao/scholaraio --skill paper-guided-reading -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install ZimoLiao/scholaraio paper-guided-reading --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/ZimoLiao/scholaraio.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/.claude/skills/paper-guided-reading .opencode/skills/paper-guided-reading && 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 "paper-guided-reading" agent skill from https://github.com/ZimoLiao/scholaraio/tree/main/.claude/skills/paper-guided-reading into .opencode/skills/paper-guided-reading/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "paper-guided-reading", 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
paper-guided-reading- GitHub stars
- 577
- Token cost
- ~968 tokens
- SKILL.md length
- 198 words
- Files
- 1
- Skills in repo
- 43
- Repo updated
- First seen
- Licence
- MIT
At a glance
A skill your agent uses when the user wants guided reading, deep reading, or structured analysis of a single paper, starting from fuzzy keywords or a research question.
- Works in 6 steps: 本地检索与摘要初筛 → 意图确认与分支处理 → 全文加载与预检 → …
- The user wants guided reading
- SKILL.md covers 核心原则, 执行逻辑, 示例 and 学术态度
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Paper Guided Reading is an agent skill from ZimoLiao/scholaraio. Use when the user wants guided reading, deep reading, or structured analysis of a single paper, starting from fuzzy keywords or a research question.
Its SKILL.md is about 970 tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Hypothesis generation. The repository describes itself as: Scholar All-In-One: A research infrastructure for AI agents. The licence is MIT.
When your agent uses it
- The user wants guided reading
- Structured analysis of a single paper
- Starting from fuzzy keywords
- A research question
Example prompts
- “/paper-guided-reading”
Requirements
- Python 3
Workflow steps
6 steps, taken from the step headings in SKILL.md.
What it can do on your machine
Read from SKILL.md and the folder at commit 777628b. 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 bash and markdown).
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
Paper Guided Reading loads about 968 tokens when it runs. Until then it costs about 42 tokens; SKILL.md has 198 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
The full file from ZimoLiao/scholaraio at commit 777628b, republished under its MIT licence (© ZimoLiao). 198 words, ~968 tokens.
Download SKILL.mdSave it as
.claude/skills/paper-guided-reading/SKILL.md (or your agent's skills folder).- name
- paper-guided-reading
- description
- Use when the user wants guided reading, deep reading, or structured analysis of a single paper, starting from fuzzy keywords or a research question.
引导式论文检索与精读
当用户给出模糊的关键词、问题或研究兴趣时，扮演一位耐心的研究伙伴：先在本地知识库中检索候选论文，通过摘要筛选与用户确认目标，再调取全文进行结构化精读分析，最终以对话形式输出见解，并随时准备回答用户的后续问题。
核心原则
- 当前 Agent 原生能力优先，但必须先做能力检查：按论文来源和证据契约路由，不按 Agent 品牌路由。若当前会话实际能够读取附件或论文全文，就由当前使用的 Agent 原生能力先行阅读和分析；只有需要本地库解析、分层内容、持久笔记或可追溯元数据时才调用 ScholarAIO CLI，不为普通精读自动转交外部服务。
- 不写完整报告：分析结果以结构化对话要点呈现，不生成长篇 Markdown 报告文件。
- 先检索、后确认、再精读：避免在信息模糊时直接假设目标论文。
- 证据先行：所有论断必须基于原文（L4 全文、图表、公式）。
- 灰暗诚实：敢于指出方法缺陷、过度宣称和逻辑漏洞。
- 教学相长：用户提问时，用原文证据解释，必要时编写代码辅助理解。
执行逻辑
1. 本地检索与摘要初筛
接收用户的模糊输入（关键词、研究问题、方法名称、作者片段等），在本地库执行多维度检索：
# 关键词检索
scholaraio search "<关键词>" --limit 10
# 语义检索（推荐与关键词检索并用）
scholaraio usearch "<用户描述>" --limit 10
# 若用户提到作者
scholaraio search-author "<作者名>" --limit 10读取候选论文的 L1（元数据）和 L2（摘要），快速评估相关性。 向用户呈现 3-5 篇最相关候选 的精简信息（标题、作者、年份、期刊/会议、摘要核心句），并询问：
- "这些论文中是否有你想深入了解的？"
- "你的具体兴趣点是什么？"（例如：方法细节、实验设计、某定理/公式、应用前景）
- "是否需要进一步缩小范围？"
2. 意图确认与分支处理
分支 A：用户确认或指向了具体论文
- 记录用户明确的目标论文 ID（目录名 / UUID / DOI）
- 记录用户的特定关注点（如有）
- 进入第 3 步（全文精读）
分支 B：用户表示本地结果不匹配
- 询问用户期望的方向更具体的信息
- 若仍无法匹配，提议外部探索：
- "本地库中没有明显匹配的论文，你是否希望我通过 arXiv、宿主原生网页搜索或 OpenAlex 探索 来寻找相关文献？"
- 必须获得用户明确同意后再行动
- 经同意后，调用
/arxiv、/explore或宿主原生网页搜索进行外部检索与下载
3. 全文加载与预检
确认目标论文后，加载全文及辅助信息：
scholaraio show "<paper-id>" --layer 2 # 摘要
scholaraio show "<paper-id>" --layer 3 # 结论（如已 enrich）
scholaraio show "<paper-id>" --layer 4 # 全文 markdown同时检查：
- 已有
notes.md：复用历史分析笔记，避免重复劳动 images/目录：建立图表索引，对关键图片打开确认内容
4. 结构化精读分析
依据 docs/writing-guide/paper-reading-framework.md 的 20 条框架进行系统性分析，但以对话式要点输出，重点回应用户在第 2 步中提到的关注点。
分析维度如下（根据用户兴趣有侧重地展开）：
- 文献信息：作者、年份、标题、期刊/会议、DOI
- 核心科学问题：论文试图解决什么问题？
- 核心假设：作者依赖的理论前提是什么？
- 研究设计：实验设计或理论框架的整体结构
- 数据/样本：数据来源、规模、代表性、潜在偏差
- 方法与技术：核心方法、创新点、与已有方法的区别
- 分析流程：从输入到输出的关键步骤
- 数据分析：统计方法、度量指标、显著性检验
- 核心发现：最重要的 1-3 个发现
- 实验结果：定量/定性结果总结
- 辅助结果：补充实验、消融实验、敏感性分析
- 最终结论：作者如何总结自己的贡献
- 领域贡献：该研究在领域中的位置
- 与用户研究的关联：结合用户第 2 步给出的方向，评估可迁移性
- 综述亮点：值得在文献综述中强调的要点
- 图表索引：关键 Figure/Table 的内容核实与解读
- 方法严谨性评价：设计是否合理、控制是否充分
- 疑问与不足：逻辑漏洞、过度宣称、未解决的问题
- 启发与未来方向：对用户研究的潜在启发
- 代表性参考文献：文中引用的奠基性工作
输出形式：
- 先给出一句话核心贡献总结
- 再围绕用户关注点展开 3-5 个结构化要点
- 若用户无特定关注点，则优先覆盖：核心问题、方法创新、关键发现、主要局限
多模态验证：
- 图表：打开
images/中的关键图片，确认坐标轴、样本量、误差棒、趋势 - 公式：提取 L4 中的 LaTeX 公式，必要时写 Python 代码验证推导或数值
- 代码：检查论文是否提及公开代码/数据，如有则尝试解释或运行
跨论文关联（可选）： 若知识库中存在相关论文，可简要调用对比：
scholaraio refs "<paper-id>"
scholaraio citing "<paper-id>"
scholaraio shared-refs "<paper-id>" "<相关论文id>"重点关注：结论是否一致、方法差异、可迁移性。
5. 对话式教学问答
完成首轮分析后，主动邀请用户提问：
- "你对这篇论文的哪个部分最感兴趣？我可以进一步展开。"
- "有没有哪个公式、实验或结论你想深入讨论？"
回答用户问题时：
- 必须引用原文段落、图表编号或公式作为证据
- 将复杂概念拆解为可理解的步骤
- 必要时编写并运行 Python/R 代码进行演示或验证
- 敢于提出反方观点："不过这里有一个值得注意的问题..."
6. 持久化 T2 笔记
将跨会话值得保留的发现写入论文目录的 notes.md：
scholaraio show "<paper-id>" --append-notes "## YYYY-MM-DD | paper-guided-reading | <用户关注的主题>
- 核心发现：...
- 方法特点：...
- 关键局限：...
- 与用户研究的关联：..."笔记格式：
## YYYY-MM-DD | paper-guided-reading | <用户关注的主题>
- 核心发现：...
- 方法特点：...
- 关键局限：...
- 与用户研究的关联：...示例
用户："我想了解一下关于大模型幻觉检测的最新方法"
→ scholaraio search + scholaraio usearch 检索本地库 → 呈现 3-5 篇候选摘要 → 询问用户具体想深入了解哪一篇
用户："第二篇看起来比较相关，我想知道它的评估指标设计是否合理" → 加载该论文 L4 → 定位评估指标相关章节和图表 → 按 20 条框架重点分析 P8/P16/P17 → 对话输出：指标设计的合理性与潜在问题 → 邀请进一步提问
用户："这些都不是我想要的，我想找的是医疗领域的幻觉检测"
→ 确认本地结果不匹配 → 提议："是否允许我通过 arXiv 和网页搜索寻找医疗领域相关论文？" → 经同意后调用 /arxiv 和宿主原生网页搜索
学术态度
- 论文结论是作者的宣称，不是真理。
- 不迷信权威：顶刊论文也可能存在方法缺陷或过度泛化。
- 交叉验证：当多篇论文结论相左时，主动指出分歧并分析可能原因。
- 区分事实与观点：明确标注哪些是实验数据支持的结论，哪些是作者的推测或解读。
- 通过举证和辩论，帮助用户更接近科学真相，而非简单复述文献。
© ZimoLiao, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in .claude/skills/paper-guided-reading of ZimoLiao/scholaraio.
Open the folder on GitHubat commit 777628b
Compare with similar skills
Paper Guided Reading 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 |
|---|---|---|---|---|---|---|
| Paper Guided Reading this skillZimoLiao/scholaraio | 577 | — | ~968 | Automated safety check: Pass | MIT | |
| 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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Categories
Questions about Paper Guided Reading
What does Paper Guided Reading do?
A skill your agent uses when the user wants guided reading, deep reading, or structured analysis of a single paper, starting from fuzzy keywords or a research question. Paper Guided Reading is an agent skill from ZimoLiao/scholaraio. Use when the user wants guided reading, deep reading, or structured analysis of a single paper, starting from fuzzy keywords or a research question.
When should I use Paper Guided Reading?
Paper Guided Reading fits situations like: the user wants guided reading; structured analysis of a single paper; starting from fuzzy keywords; A research question.
How do I install Paper Guided Reading in Claude Code?
Run `npx skills add ZimoLiao/scholaraio --skill paper-guided-reading -a claude-code`. Or copy the skill folder (.claude/skills/paper-guided-reading in ZimoLiao/scholaraio) into .claude/skills/paper-guided-reading in your project. Claude Code loads it when a task matches its description.
How do I install Paper Guided Reading in Codex?
Run `npx skills add ZimoLiao/scholaraio --skill paper-guided-reading -a codex`. Or copy the skill folder (.claude/skills/paper-guided-reading in ZimoLiao/scholaraio) into .agents/skills/paper-guided-reading in your project. Codex loads it when a task matches its description.
Can I use Paper Guided Reading 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 ZimoLiao/scholaraio --skill paper-guided-reading -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/paper-guided-reading, .gemini/skills/paper-guided-reading, .github/skills/paper-guided-reading and .opencode/skills/paper-guided-reading in your project.
What does Paper Guided Reading need to run?
SKILL.md names no scripts, command-line tools or credentials: Paper Guided Reading is instructions for the agent only. Our summary lists: Python 3.
Does Paper Guided Reading 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 Paper Guided Reading 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 Paper Guided Reading use?
Paper Guided Reading is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Paper Guided Reading use?
About 968 tokens (SKILL.md is roughly 3.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Paper Guided Reading?
Skills that share tags, products or a category with Paper Guided Reading: 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 Paper Guided Reading?
ZimoLiao (a GitHub user) maintains it in ZimoLiao/scholaraio, which has 577 GitHub stars. The repository holds 43 skills in this directory. The repository was last updated on September 25, 2026.
Source: ZimoLiao/scholaraio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.