# Session Log 9: LaTeX Template Integration and Draft 0 Development from Outline v4

**Date**: September 3, 2025  
**Focus**: Integration of outline_v4.md content into Agents4Science 2025 LaTeX template, iterative expansion of sections based on mentor feedback, and establishment of Draft 0 as foundation for paper development

## Session Overview

This session focused on transforming the detailed paper outline (outline_v4.md) and mentor feedback into an initial LaTeX draft using the Agents4Science 2025 conference template. The key achievement was establishing Draft 0 with basic structure and content from the outline, then iteratively expanding sections while identifying gaps and areas requiring further development. This represents the critical transition from planning to actual paper writing.

## Session Context and Continuation Point

**Previous Status**: Had complete experimental results (H1-H6) organized in `idea_14_workspace/outputs/` and outline prepared at `papers/outline_v4.md` with detailed structure and key findings. Mentor notes provided guidance on paper direction and emphasis.

**Current Session Goal**: Create Draft 0 by integrating outline content into proper LaTeX template, then expand and refine based on outline coverage analysis.

**Key Input Files Used**:
- `papers/outline_v4.md` - Primary source for paper structure and content
- `hypotheses_suites/final_hypotheses_20250825_180000.json` - H1-H6 experimental details
- `idea_14_workspace/outputs/visualisation/tables/table_2_fnr_comparison.csv` - Real data for tables
- `papers/latex_paper_templates/Agents4Science_Template 2/agents4science_2025.tex` - Original template
- `papers/latex_paper_templates/Agents4Science_Template 2/agents4science_2025.sty` - Style file

## Major Accomplishments

### 1. Initial Template Setup and Outline Integration

**Phase A - Basic Template Configuration:**
- Reviewed Agents4Science 2025 template requirements and figure formatting guidelines
- Analyzed `agents4science_2025.tex` and `agents4science_2025.sty` files for compliance requirements
- Updated `src/visualisation/plot_utils.py` font settings (Times New Roman, 10pt) to match template
- **Created**: `papers/latex_paper_templates/Agents4Science_Template 2/consistency_confound_paper.tex` as working document

**Phase B - Simple Outline Material Transfer:**
- Copied abstract directly from outline_v4.md
- Transferred introduction structure with three core claims
- Added basic methodology sections (threat model, detection methods, experimental setup)
- Integrated key results from H1 and H2 sections
- Added consistency confound definition from outline Section 5

### 2. Iterative Expansion Based on Mentor Feedback

**First Expansion - Real Data Integration:**
- Replaced placeholder data in tables with actual experimental results
- Populated Table 2 (FNR@5%FPR comparison) from CSV files
- Added specific AUROC and FNR values from JSON result files
- Integrated actual threshold values and actual_fpr for transparency

**Second Expansion - Methodology Enhancement:**
- Expanded rationale for black-box SE variant based on mentor notes
- Added detailed explanation of embedding-based clustering choice
- Clarified differences from original NLI-based approach
- Added Table 1 comparing SE implementation variants

**Third Expansion - Citation and Reference Fixes:**
- Fixed LaTeX compilation errors from incorrect `\bibitem{}` usage
- Converted to numbered reference format matching template
- Ensured all citations properly formatted

### 3. Critical Gap Identification Through Outline Matching

**Coverage Analysis Against outline_v4.md:**
- ✅ Abstract and Introduction (Sections 1-2)
- ✅ Basic Results (Section 3.1, 3.2)
- ⚠️ Partial Coverage: Investigating Failure Modes (Section 4)
  - Initially missing H3 (length analysis)
  - Initially missing H4 (brittleness analysis)  
  - **Completely missing H5 (paraphrase analysis)**
- ⚠️ Partial Coverage: Consistency Confound (Section 5)
  - Missing subsection 5.2 (Why SE is Uniquely Vulnerable)
  - Missing subsection 5.4 (Qualitative Examples)

**Gap Resolution Actions:**
- Added comprehensive H5 paraphrase experiment section
- Integrated H3 and H4 analysis into "Investigating failure modes" subsection
- Expanded figure captions with detailed explanations
- Added Figure 4 for paraphrase analysis results

### 4. Figure Management and Formatting Issues

**Figure Placement Problems Identified:**
- Figures appearing far from reference points due to LaTeX float algorithm
- Initial `[h]` placement too restrictive for high figure density
- Figure numbering confusion after adding paraphrase figure

**Solutions Implemented:**
- Changed all figures from `[h]` to `[!htbp]` for better placement control
- Renumbered figures sequentially (1-5) after adding paraphrase figure
- Fixed LaTeX math symbols in captions (`Δ` → `$\Delta$`, `≈` → `$\approx$`)
- Ensured proper figure order matches text flow

### 5. Content Enhancement from Experimental Results

**Data-Driven Expansions:**
- Added specific performance numbers throughout (e.g., R²=0.103 for length correlation)
- Integrated brittleness quantification (41% FNR increase from τ=0.1 to 0.2)
- Added paraphrase experiment results (-6.3pp BERTScore, -2.0pp Embedding Variance)
- Included consistency confound attribution rates (73.3% Llama, 97.5% Qwen)

**Methodological Details Added:**
- Experimental parameters: N=5, T=0.7, top-p=0.95, max_tokens=1024
- Embedding model specifics: Alibaba-NLP/gte-large-en-v1.5
- Clustering approach: Agglomerative with average linkage
- Evaluation protocol: FNR@5%FPR with canonical τ=0.2

## Current Paper Status: Draft 0

### What We Have:
- **Complete Sections**: Introduction, methodology, core results (H1-H2), failure mode analysis (H3-H5)
- **Populated Tables**: Table 1 (SE variants comparison), Table 2 (FNR comparison with real data)
- **Complete Figures**: 5 figures with proper placement (`[!htbp]`) and detailed captions
- **Basic Coverage**: Consistency confound mechanism and quantitative validation (73.3%, 97.5%)
- **Proper Formatting**: LaTeX template compliance, math symbols fixed (`$\Delta$`, `$\approx$`)
- **Template Compliance**: Both required checklists included (lines 288-491)

### What's Still Needed for Draft 1:
- **Section Enhancement**: Expand consistency confound with missing subsections from outline:
  - 5.2: Why SE is Uniquely Vulnerable (two-step process explanation)
  - 5.4: Qualitative examples (jbb_75 phishing, h2_harmful_061 SQL injection)
- **Discussion Expansion**: Broader implications and future work (currently basic)
- **Statistical Enhancement**: Confidence intervals and significance testing
- **Checklist Completion**: Fill out `\answerTODO{}` and `\justificationTODO{}` macros
- **Final Verification**: Cross-check all numbers against source files in `outputs/`

## Technical Issues Resolved

### 1. LaTeX Compilation Errors
- Fixed "Lonely \item" errors from incorrect bibliography format
- Resolved unicode character issues in figure captions
- Corrected figure environment syntax errors

### 2. Content Accuracy Corrections
- Corrected misinterpretation of SE application (not previously applied to jailbreaks)
- Fixed understanding of paraphrase experiment (data contamination, not prompt evasion)
- Aligned methodology description with actual implementation

### 3. Figure Integration Challenges
- Resolved figure numbering after adding new Figure 4
- Fixed placement issues with `[!htbp]` modification
- Ensured all figures properly referenced in text

## Next Steps for Paper Development

### Immediate Tasks (Draft 0 → Draft 1):
1. **Complete Missing Sections**:
   - Add Section 5.2 on SE's unique vulnerability
   - Add Section 5.4 with qualitative examples
   - Expand discussion with limitations

2. **Content Refinement**:
   - Ensure consistent terminology throughout
   - Verify all numbers match source files
   - Add cross-references between sections

3. **Statistical Enhancement**:
   - Add confidence intervals where possible
   - Include significance testing for key claims
   - Address statistical requirements in checklist

### Future Development (Draft 1 → Submission):
1. **Writing Quality**:
   - Improve flow and transitions
   - Strengthen argument structure
   - Polish abstract and introduction

2. **Technical Completeness**:
   - Add supplementary materials section
   - Complete reproducibility documentation
   - Ensure all code/data references accurate

3. **Final Formatting**:
   - Verify page limits (8 pages main content)
   - Check figure/table quality at publication resolution
   - Complete all required checklists

## Key Insights and Decisions

### 1. Iterative Development Approach
Successfully used outline as scaffold, then progressively expanded with real data and additional detail rather than trying to write complete sections initially.

### 2. Gap Analysis Value
Systematic comparison with outline_v4.md revealed missing H5 section and other gaps that would have compromised paper completeness.

### 3. Template Compliance Priority
Early attention to LaTeX formatting requirements prevented major restructuring later and ensured professional presentation from Draft 0.

## Files Created and Modified

**Primary Output**:
- `papers/latex_paper_templates/Agents4Science_Template 2/consistency_confound_paper.tex` (491 lines)

**Modified Files**:
- `src/visualisation/plot_utils.py` - Updated font settings for LaTeX compatibility

**Key Reference Files Used**:
- `papers/outline_v4.md` - Source for all section content and structure
- `hypotheses_suites/final_hypotheses_20250825_180000.json` - H1-H6 experimental specifications
- `idea_14_workspace/outputs/visualisation/tables/table_2_fnr_comparison.csv` - Real FNR data for Table 2
- Figure references: `figures_and_tables/figures/figure_[1-5]_*.png` (5 figures)

## Continuation Notes for Next Session

**Immediate Tasks to Complete Draft 1**:
1. **Add Missing Content from outline_v4.md**:
   - Section 5.2: "Why SE is Uniquely Vulnerable" (lines 100-101 in outline)
   - Section 5.4: "Qualitative Examples" (lines 108-110 in outline)
   - Specific examples: jbb_75 (phishing), h2_harmful_061 (SQL injection)

2. **Complete Template Requirements**:
   - Fill all `\answerTODO{}` macros in AI Involvement Checklist (lines 311-334)
   - Fill all `\answerTODO{}` macros in Paper Checklist (lines 368-477)
   - Add `\justificationTODO{}` explanations for each answer

3. **Verify Data Accuracy**:
   - Cross-reference all performance numbers against source files in `outputs/h1-h6/`
   - Ensure figure file names match actual generated figures
   - Validate all experimental parameters match configs

**Current State Assessment**:
- **Content Completeness**: ~75% (missing 2 subsections from outline)
- **Template Compliance**: 90% (checklists present but unfilled)
- **Formatting Quality**: 95% (figures fixed, math symbols corrected)
- **Data Integration**: 100% (all tables populated with real data)

**Key Achievement**: Successfully established Draft 0 with comprehensive experimental integration (H1-H5), proper LaTeX formatting, and clear identification of remaining work needed for submission readiness.

**Next Session Priority**: Complete missing outline sections 5.2 and 5.4, then fill mandatory checklists to achieve Draft 1 status.