Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application.
$ npx skills add aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aipoch/medical-research-skills clinical-diagnostic-reasoning --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/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/scientific-skills/Other/clinical-diagnostic-reasoning .claude/skills/clinical-diagnostic-reasoning && 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 "clinical-diagnostic-reasoning" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/clinical-diagnostic-reasoning into .claude/skills/clinical-diagnostic-reasoning/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-diagnostic-reasoning", 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/aipoch/medical-research-skills/tree/main/scientific-skills/Other/clinical-diagnostic-reasoningType 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 aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aipoch/medical-research-skills clinical-diagnostic-reasoning --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/scientific-skills/Other/clinical-diagnostic-reasoning .agents/skills/clinical-diagnostic-reasoning && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "clinical-diagnostic-reasoning" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/clinical-diagnostic-reasoning into .agents/skills/clinical-diagnostic-reasoning/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-diagnostic-reasoning", 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 aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aipoch/medical-research-skills clinical-diagnostic-reasoning --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/scientific-skills/Other/clinical-diagnostic-reasoning .cursor/skills/clinical-diagnostic-reasoning && 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 "clinical-diagnostic-reasoning" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/clinical-diagnostic-reasoning into .cursor/skills/clinical-diagnostic-reasoning/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-diagnostic-reasoning", 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/aipoch/medical-research-skills.git --path scientific-skills/Other/clinical-diagnostic-reasoning--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 aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aipoch/medical-research-skills clinical-diagnostic-reasoning --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/scientific-skills/Other/clinical-diagnostic-reasoning .gemini/skills/clinical-diagnostic-reasoning && 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 "clinical-diagnostic-reasoning" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/clinical-diagnostic-reasoning into .gemini/skills/clinical-diagnostic-reasoning/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-diagnostic-reasoning", 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 aipoch/medical-research-skills clinical-diagnostic-reasoningInstalls 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 aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/scientific-skills/Other/clinical-diagnostic-reasoning .github/skills/clinical-diagnostic-reasoning && 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 "clinical-diagnostic-reasoning" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/clinical-diagnostic-reasoning into .github/skills/clinical-diagnostic-reasoning/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-diagnostic-reasoning", 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 aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aipoch/medical-research-skills clinical-diagnostic-reasoning --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/scientific-skills/Other/clinical-diagnostic-reasoning .opencode/skills/clinical-diagnostic-reasoning && 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 "clinical-diagnostic-reasoning" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Other/clinical-diagnostic-reasoning into .opencode/skills/clinical-diagnostic-reasoning/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "clinical-diagnostic-reasoning", 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.
clinical-diagnostic-reasoningIdentify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application.
Clinical Diagnostic Reasoning is an agent skill from aipoch/medical-research-skills. Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application. For diagnostic reasoning, treatment decisions, and
Its SKILL.md is about 2.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files (for example `POLISH_CHANGELOG.md` and `eval_report_clinical-diagnostic-reasoning_result.json`).
It sits in Research & Science. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.
Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.
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.
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
No URLs in SKILL.md.
From URLs in SKILL.md, links to its own repository left out.
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Clinical Diagnostic Reasoning loads about 2.8k tokens when it runs. Until then it costs about 55 tokens; SKILL.md has 914 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.
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.
The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 914 words, ~2,803 tokens.
.claude/skills/clinical-diagnostic-reasoning/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.Improve diagnostic accuracy and treatment decisions by recognizing and overcoming systematic cognitive errors in clinical thinking.
✅ Use for:
❌ NOT for:
New patient presentation
↓
┌───[Gather information through language/history]
│ ↓
│ Does presentation suggest standard algorithm?
│ ├─ NO → Continue hypothesis generation
│ │ ↓
│ │ Develop differential diagnosis
│ │ ↓
│ │ [Proceed to bias check]
│ │
│ └─ YES → Does patient context match algorithm assumptions?
│ ├─ YES → Apply algorithm
│ │ ↓
│ │ Monitor outcomes
│ │ ↓
│ │ [Proceed to bias check]
│ │
│ └─ NO → What patient-specific factors differ?
│ ↓
│ Does evidence justify deviation?
│ ├─ YES → Document rationale and modify
│ └─ NO → Apply algorithm; reconsider if new data
│
└─── [BIAS CHECK - Always perform]
↓
Am I anchored to initial impression?
├─ POSSIBLY → Reassess case without initial anchor
│
Have I found one explanation and stopped searching?
├─ YES → Continue search: "What else could this be?"
│ "Does this explain ALL findings?"
│
Am I pattern-matching from recent/memorable case?
├─ YES → List specific differences between cases
│
Am I stereotyping this patient?
├─ POSSIBLY → Reset: Evaluate symptoms independently
│
Do I feel compelled to "do something"?
├─ YES → Is action justified by evidence or anxiety?
│ Is watchful waiting appropriate?
│
Have I sought disconfirming evidence?
└─ NO → Actively look for data that contradicts working diagnosisClinical error occurred
↓
What was the error?
├─ Wrong diagnosis
├─ Inappropriate treatment
└─ Missed diagnosis
↓
Was this a knowledge gap or thinking error?
├─ KNOWLEDGE GAP → Address through study
│ (Not the focus of this skill)
│
└─ THINKING ERROR → Which cognitive bias operated?
↓
┌─ Anchoring? (stuck on initial impression)
├─ Satisfaction of search? (stopped too early)
├─ Availability? (recent case pattern-match)
├─ Attribution? (stereotyped patient)
└─ Commission? (unnecessary action)
↓
Was error preventable with current knowledge?
├─ YES → How could bias have been recognized?
│ ↓
│ Extract generalizable lesson
│ ↓
│ Apply to future similar situations
│
└─ NO → Document for learning, not applicableNeed to present medical information
↓
What decision does patient need to make?
↓
Identify equivalent framings:
- Positive frame (% success/survival)
- Negative frame (% failure/mortality)
- Absolute numbers
- Relative risk
↓
Which framing facilitates genuine understanding?
↓
Is my framing choice unintentionally biasing decision?
├─ YES → Present multiple equivalent framings
│ Allow patient to process from different angles
│
└─ UNCERTAIN → Present both positive and negative frames
Verify patient comprehension
↓
"What is your understanding of the risks/benefits?"Novice approach: Finds one clinically interesting explanation and stops diagnostic inquiry. "The patient has pneumonia, that explains the fever and cough."
Expert approach: After finding initial explanation, explicitly asks: "What else could be present? Does this explain ALL findings? Could there be a coexisting condition?"
Timeline: Develops over years of clinical experience through cases where initial findings were incomplete or coincidental. Critical moment comes when missing a second diagnosis causes patient harm—realization that "not finding everything is suboptimal."
Novice approach: Initial symptoms or emergency department triage note establishes diagnosis that persists despite contradictory information. "ED said anxiety attack, so I'm treating anxiety."
Expert approach: Periodically resets evaluation without reference to initial impressions. "If I saw this patient fresh right now, what would I think?" Actively seeks information contradicting initial hypothesis.
Timeline: Requires recognizing pattern across multiple cases where initial impression proved misleading. Breakthrough occurs when physician catches themselves defending an anchor despite mounting contrary evidence.
Novice approach: Feels compelled to take action because "doing something" feels better than watchful waiting, even without clear indication. Treats borderline abnormal labs, adjusts medications unnecessarily.
Expert approach: Explicitly evaluates whether action is justified by evidence or driven by psychological need to intervene. Comfortable with watchful waiting when appropriate. Asks: "Will treatment help more than harm?"
Timeline: Often develops after causing harm through unnecessary intervention. Turning point is recognizing that action carries its own risks and that inaction is sometimes the most appropriate decision.
Novice approach: "I just saw three patients with Lyme disease, so this patient's fatigue must be Lyme too." Pattern-matches based on superficial similarities without considering differences.
Expert approach: When noticing similarity to recent case, explicitly lists differences: "How is this patient NOT like that case?" Questions whether similarities are clinically meaningful or coincidental.
Timeline: Accumulates through experience with similar-seeming cases that proved different. Key insight comes when a "just like the last patient" case turns out completely different upon deeper investigation.
Novice approach: Accepts colleague's characterization that patient is "drug-seeking" or "anxious" and dismisses symptoms without independent evaluation. Stereotypes based on demographics.
Expert approach: Approaches each patient as individual regardless of others' characterizations. "What does THIS patient's presentation tell me?" Separates objective findings from attributed motivations.
Timeline: Often requires personal experience of misjudging a patient or discovering that a dismissed patient had serious pathology. Recognition that stereotypes prevented seeing actual clinical presentation.
Novice approach: Either follows algorithms without contextual consideration ("The guideline says X, so I must do X") OR abandons them based on gut feeling without justification.
Expert approach: Recognizes algorithms as population-based tools requiring interpretation. Can articulate why specific patient context justifies deviation when it does. Documents reasoning.
Timeline: Develops through repeated experience applying guidelines to diverse patients. Critical learning occurs when rigid application causes harm OR when appropriate deviation leads to better outcome—recognizing that expertise lies in knowing which mode applies when.
Novice says: "The patient has [single diagnosis]" Expert says: "The primary issue is [diagnosis], but I'm also considering [alternatives] and haven't ruled out [other possibilities]"
Novice says: "We need to do something" Expert says: "The question is whether intervention offers more benefit than harm compared to watchful waiting"
Novice says: "The protocol says..." Expert says: "The protocol applies when [conditions], but this patient differs in [specific ways]"
Clinical reasoning requires navigating between two extremes:
Cognitive biases are predictable traps on the diagnostic path:
This skill accepts requests that match the documented purpose of clinical-diagnostic-reasoning and include enough context to complete the workflow safely.
Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:
clinical-diagnostic-reasoningonly handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.
© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
SKILL.md and 2 other files in scientific-skills/Other/clinical-diagnostic-reasoning of aipoch/medical-research-skills.
Open the folder on GitHubat commit 686e09d
Clinical Diagnostic Reasoning 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 |
|---|---|---|---|---|---|---|
| Clinical Diagnostic Reasoning this skillaipoch/medical-research-skills | 1.9k | — | ~2.8k | Automated safety check: Pass | MIT | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| GitHub Deep Researchbytedance/deer-flow | 84k | 4 repos | ~1.3k | Automated safety check: Pass | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Content Research Writerweapp-tailwindcss/weapp-tailwindcss | 1.9k | 25 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Last30daysmvanhorn/last30days-skill | 64k | — | ~7.9k | Automated safety check: Notes | MIT |
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
bytedance/deer-flow
Researches a GitHub repository over four rounds using the GitHub API and web search, then writes a structured markdown report with timeline, metrics and Mermaid diagrams.
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.
weapp-tailwindcss/weapp-tailwindcss
Assists in writing high-quality content by conducting research, adding citations, improving hooks, iterating on outlines, and providing real-time feedback on each section.
mvanhorn/last30days-skill
Research what people actually say about any topic in the last 30 days.
spacering-net/codeg
Structured manuscript/grant review with checklist-based evaluation.
aipoch/medical-research-skills
Complete workflow for generating academic research posters from PDF literature; use when you need to extract paper content from PDFs and produce a LaTeX-based poster…
aipoch/medical-research-skills
Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool.
aipoch/medical-research-skills
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
aipoch/medical-research-skills
A toolkit for preparing ISO 13485:2016 certification documentation for medical device QMS.
aipoch/medical-research-skills
Recommends target journals for manuscript submission by analyzing the paper topic/abstract and the journal distribution of similar PubMed literature; use when users ask for journal…
aipoch/medical-research-skills
Creates academic-poster writing packages for LaTeX using beamerposter, tikzposter, or baposter.
Categories
Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application. Clinical Diagnostic Reasoning is an agent skill from aipoch/medical-research-skills. Identify and counteract cognitive biases in medical decision-making through systematic error analysis and contextual algorithm application.
Clinical Diagnostic Reasoning fits situations like: research & Science work in your project.
Run `npx skills add aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a claude-code`. Or copy the skill folder (scientific-skills/Other/clinical-diagnostic-reasoning in aipoch/medical-research-skills) into .claude/skills/clinical-diagnostic-reasoning in your project. Claude Code loads it when a task matches its description.
Run `npx skills add aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a codex`. Or copy the skill folder (scientific-skills/Other/clinical-diagnostic-reasoning in aipoch/medical-research-skills) into .agents/skills/clinical-diagnostic-reasoning in your project. Codex loads it when a task matches its description.
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill clinical-diagnostic-reasoning -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/clinical-diagnostic-reasoning, .gemini/skills/clinical-diagnostic-reasoning, .github/skills/clinical-diagnostic-reasoning and .opencode/skills/clinical-diagnostic-reasoning in your project.
SKILL.md names no scripts, command-line tools or credentials: Clinical Diagnostic Reasoning is instructions for the agent only.
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.
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.
Clinical Diagnostic Reasoning is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
About 2.8k tokens (SKILL.md is roughly 11k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
Skills that share tags, products or a category with Clinical Diagnostic Reasoning: Hypothesis Generation (spacering-net/codeg, 3.9k stars), GitHub Deep Research (bytedance/deer-flow, 84k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars) and Content Research Writer (weapp-tailwindcss/weapp-tailwindcss, 1.9k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,937 GitHub stars. The repository holds 578 skills in this directory. The repository was last updated on September 17, 2026.
Source: aipoch/medical-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.