Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design expe
Install
The skill file stays in the publisher's repository.
Paste the copied command in a terminal. It installs this SKILL.md into that agent.
npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill hypothesis-generation -a cursor -y
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
Questions
How do I install hypothesis-generation?
Download skills/03-K-Dense-AI-claude-scientific-skills/hypothesis-generation/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does hypothesis-generation live?
The publisher keeps it at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.
Which agents can use hypothesis-generation?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.
Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
name: hypothesis-generation
description: Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.
allowed-tools: Read Write Edit Bash
license: MIT license
metadata:
skill-author: K-Dense Inc.
Scientific Hypothesis Generation
Overview
Hypothesis generation is a systematic process for developing testable explanations. Formulate evidence-based hypotheses from observations, design experiments, explore competing explanations, and develop predictions. Apply this skill for scientific inquiry across domains.
When to Use This Skill
This skill should be used when:
Developing hypotheses from observations or preliminary data
Designing experiments to test scientific questions
Exploring competing explanations for phenomena
Formulating testable predictions for research
Conducting literature-based hypothesis generation
Planning mechanistic studies across scientific domains
Visual Enhancement with Scientific Schematics
⚠️ MANDATORY: Every hypothesis generation report MUST include at least 1-2 AI-generated figures using the scientific-schematics skill.
This is not optional. Hypothesis reports without visual elements are incomplete. Before finalizing any document:
Generate at minimum ONE schematic or diagram (e.g., hypothesis framework showing competing explanations)
Any complex concept that benefits from visualization
For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
Workflow
Follow this systematic process to generate robust scientific hypotheses:
1. Understand the Phenomenon
Start by clarifying the observation, question, or phenomenon that requires explanation:
Identify the core observation or pattern that needs explanation
Define the scope and boundaries of the phenomenon
Note any constraints or specific contexts
Clarify what is already known vs. what is uncertain
Identify the relevant scientific domain(s)
2. Conduct Comprehensive Literature Search
Search existing scientific literature to ground hypotheses in current evidence. Use both PubMed (for biomedical topics) and general web search (for broader scientific domains):
For biomedical topics:
Use WebFetch with PubMed URLs to access relevant literature
Search for recent reviews, meta-analyses, and primary research
Look for similar phenomena, related mechanisms, or analogous systems
For all scientific domains:
Use WebSearch to find recent papers, preprints, and reviews
Search for established theories, mechanisms, or frameworks
Identify gaps in current understanding
Search strategy:
Begin with broad searches to understand the landscape
Narrow to specific mechanisms, pathways, or theories
Look for contradictory findings or unresolved debates
Consult references/literature_search_strategies.md for detailed search techniques
3. Synthesize Existing Evidence
Analyze and integrate findings from literature search:
Summarize current understanding of the phenomenon
Identify established mechanisms or theories that may apply
Note conflicting evidence or alternative viewpoints
Recognize gaps, limitations, or unanswered questions
Identify analogies from related systems or domains
4. Generate Competing Hypotheses
Develop 3-5 distinct hypotheses that could explain the phenomenon. Each hypothesis should:
Provide a mechanistic explanation (not just description)
Be distinguishable from other hypotheses
Draw on evidence from the literature synthesis
Consider different levels of explanation (molecular, cellular, systemic, population, etc.)
Strategies for generating hypotheses:
Apply known mechanisms from analogous systems
Consider multiple causative pathways
Explore different scales of explanation
Question assumptions in existing explanations
Combine mechanisms in novel ways
5. Evaluate Hypothesis Quality
Assess each hypothesis against established quality criteria from references/hypothesis_quality_criteria.md:
Testability: Can the hypothesis be empirically tested?
Falsifiability: What observations would disprove it?
Parsimony: Is it the simplest explanation that fits the evidence?
Explanatory Power: How much of the phenomenon does it explain?
Scope: What range of observations does it cover?
Consistency: Does it align with established principles?
Novelty: Does it offer new insights beyond existing explanations?
Explicitly note the strengths and weaknesses of each hypothesis.
6. Design Experimental Tests
For each viable hypothesis, propose specific experiments or studies to test it. Consult references/experimental_design_patterns.md for common approaches:
Experimental design elements:
What would be measured or observed?
What comparisons or controls are needed?
What methods or techniques would be used?
What sample sizes or statistical approaches are appropriate?
What are potential confounds and how to address them?
Consider multiple approaches:
Laboratory experiments (in vitro, in vivo, computational)
For each hypothesis, generate specific, quantitative predictions:
State what should be observed if the hypothesis is correct
Specify expected direction and magnitude of effects when possible
Identify conditions under which predictions should hold
Distinguish predictions between competing hypotheses
Note predictions that would falsify the hypothesis
8. Present Structured Output
Generate a professional LaTeX document using the template in assets/hypothesis_report_template.tex. The report should be well-formatted with colored boxes for visual organization and divided into a concise main text with comprehensive appendices.
Document Structure:
Main Text (Maximum 4 pages):
Executive Summary - Brief overview in summary box (0.5-1 page)
Competing Hypotheses - Each hypothesis in its own colored box with brief mechanistic explanation and key evidence (2-2.5 pages for 3-5 hypotheses)
IMPORTANT: Use ewpage before each hypothesis box to prevent content overflow
Each box should be ≤0.6 pages maximum
Testable Predictions - Key predictions in amber boxes (0.5-1 page)
Keep main text highly concise - only the most essential information. All details go to appendices.
Page Break Strategy:
Always use ewpage before hypothesis boxes to ensure they start on fresh pages
This prevents content from overflowing off page boundaries
LaTeX boxes (tcolorbox) do not automatically break across pages
Appendices (Comprehensive, Detailed):
Appendix A: Comprehensive literature review with extensive citations
Appendix B: Detailed experimental designs with full protocols
Appendix C: Quality assessment tables and detailed evaluations
Appendix D: Supplementary evidence and analogous systems
Colored Box Usage:
Use the custom box environments from hypothesis_generation.sty:
hypothesisbox1 through hypothesisbox5 - For each competing hypothesis (blue, green, purple, teal, orange)
predictionbox - For testable predictions (amber)
comparisonbox - For critical comparisons (steel gray)
evidencebox - For supporting evidence highlights (light blue)
summarybox - For executive summary (blue)
Each hypothesis box should contain (keep concise for 4-page limit):
Mechanistic Explanation: 1-2 brief paragraphs (6-10 sentences max) explaining HOW and WHY
Key Supporting Evidence: 2-3 bullet points with citations (most important evidence only)
Core Assumptions: 1-2 critical assumptions
All detailed explanations, additional evidence, and comprehensive discussions belong in the appendices.
Critical Overflow Prevention:
Insert ewpage before each hypothesis box to start it on a fresh page
Keep each complete hypothesis box to ≤0.6 pages (approximately 15-20 lines of content)
If content exceeds this, move additional details to Appendix A
Never let boxes overflow off page boundaries - this creates unreadable PDFs
Citation Requirements:
Aim for extensive citation to support all claims:
Main text: 10-15 key citations for most important evidence only (keep concise for 4-page limit)
Appendix A: 40-70+ comprehensive citations covering all relevant literature
Total target: 50+ references in bibliography
Main text citations should be selective - cite only the most critical papers. All comprehensive citation and detailed literature discussion belongs in the appendices. Use `
How do I install hypothesis-generation?
Download skills/03-K-Dense-AI-claude-scientific-skills/hypothesis-generation/SKILL.md from the publisher, or copy the path and open the repository. PlugMCP lists the skill and does not host the file.
Where does hypothesis-generation live?
The publisher keeps it at https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills.
Which agents can use hypothesis-generation?
Claude, Cursor, and Codex can read a SKILL.md you add from the publisher's repository.