Hypothesis Generation

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):

1. Executive Summary - Brief overview in summary box (0.5-1 page)
2. 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 \newpage before each hypothesis box to prevent content overflow
   • Each box should be ≤0.6 pages maximum
3. Testable Predictions - Key predictions in amber boxes (0.5-1 page)
4. Critical Comparisons - Priority comparison 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 \newpage 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 \newpage 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 \citep{author2023} for parenthetical citations.

LaTeX Compilation:

The template requires XeLaTeX or LuaLaTeX for proper rendering:

xelatex hypothesis_report.tex
bibtex hypothesis_report
xelatex hypothesis_report.tex
xelatex hypothesis_report.tex

Required packages: The hypothesis_generation.sty style package must be in the same directory or LaTeX path. It requires: tcolorbox, xcolor, fontspec, fancyhdr, titlesec, enumitem, booktabs, natbib.

Page Overflow Prevention:

To prevent content from overflowing on pages, follow these critical guidelines:

1. Monitor Box Content Length: Each hypothesis box should fit comfortably on a single page. If content exceeds ~0.7 pages, it will likely overflow.

2. Use Strategic Page Breaks: Insert \newpage before boxes that contain substantial content:

   \newpage
   \begin{hypothesisbox1}[Hypothesis 1: Title]
   % Long content here
   \end{hypothesisbox1}

3. Keep Main Text Boxes Concise: For the 4-page main text limit:

   • Each hypothesis box: Maximum 0.5-0.6 pages
   • Mechanistic explanation: 1-2 brief paragraphs only (6-10 sentences max)
   • Key evidence: 2-3 bullet points only
   • Core assumptions: 1-2 items only
   • If content is longer, move details to appendices

4. Break Long Content: If a hypothesis requires extensive explanation, split across main text and appendix:

   • Main text box: Brief mechanistic overview + 2-3 key evidence points
   • Appendix A: Detailed mechanism explanation, comprehensive evidence, extended discussion

5. Test Page Boundaries: Before each new box, consider if remaining page space is sufficient. If less than 0.6 pages remain, use \newpage to start the box on a fresh page.

6. Appendix Page Management: In appendices, use \newpage between major sections to avoid overflow in detailed content areas.

Quick Reference: See assets/FORMATTING_GUIDE.md for detailed examples of all box types, color schemes, and common formatting patterns.

Quality Standards

Ensure all generated hypotheses meet these standards:

• Evidence-based: Grounded in existing literature with citations
• Testable: Include specific, measurable predictions
• Mechanistic: Explain how/why, not just what
• Comprehensive: Consider alternative explanations
• Rigorous: Include experimental designs to test predictions

Resources

references/

• hypothesis_quality_criteria.md - Framework for evaluating hypothesis quality (testability, falsifiability, parsimony, explanatory power, scope, consistency)
• experimental_design_patterns.md - Common experimental approaches across domains (RCTs, observational studies, lab experiments, computational models)
• literature_search_strategies.md - Effective search techniques for PubMed and general scientific sources

assets/

• hypothesis_generation.sty - LaTeX style package providing colored boxes, professional formatting, and custom environments for hypothesis reports
• hypothesis_report_template.tex - Complete LaTeX template with main text structure and comprehensive appendix sections
• FORMATTING_GUIDE.md - Quick reference guide with examples of all box types, color schemes, citation practices, and troubleshooting tips