# Research Documentation Index

**Last Updated**: 2025-12-27
**Purpose**: Complete inventory of research documents and best practices

This index provides a comprehensive reference to all research findings, best practices, and technical investigations.

---

## Active Research Documents

`plans/research/` contains current active research and reference materials for the self-learning memory system.

### Current Research (2025)

| File | LOC | Description | Status | Category |
|------|-----|-------------|--------|----------|
| **EPISODIC_MEMORY_RESEARCH_2025.md** | 916 | December 2025 academic research findings (PREMem, GENESIS, Spatiotemporal) | 🟢 ACTIVE | Research |
| **current_implementation_analysis.md** | 408 | Current state analysis of 9 target implementations | 🟢 ACTIVE | Analysis |

### Best Practices & Reference (Active)

| File | LOC | Description | Status | Category |
|------|-----|-------------|--------|----------|
| **ets_forecasting_best_practices.md** | 1316 | ETS forecasting implementation guide with OxiDiviner | 🟢 ACTIVE | Best Practice |
| **dbscan_anomaly_detection_best_practices.md** | 1243 | DBSCAN anomaly detection guide (linfa, dbscan, cogset) | 🟢 ACTIVE | Best Practice |
| **PERFORMANCE_BENCHMARKING_BEST_PRACTICES.md** | 347 | Comprehensive benchmarking methodology and best practices | 🟢 ACTIVE | Best Practice |
| **MCP_PROTOCOL_VERSION_RESEARCH.md** | 199 | MCP 2025-11-25 protocol update analysis | 🟢 REFERENCE | Research |

---

## Archived Implementation Plans

These documents contain detailed integration plans that have been **completed**. They are kept for historical reference and understanding the implementation approach.

| File | Date | Phase | Status | Key Features |
|------|------|-------|--------|--------------|
| **PHASE1_INTEGRATION_PLAN.md** | 2025-12-25 | PREMem (Days 6-7) | ✅ COMPLETE | QualityAssessor, SalientExtractor integration, 26 atomic tasks |
| **PHASE2_INTEGRATION_PLAN.md** | 2025-12-25 | GENESIS (Day 15) | ✅ COMPLETE | CapacityManager, SemanticSummarizer integration, 4 components |
| **PHASE3_INTEGRATION_PLAN.md** | 2025-12-26 | Spatiotemporal (Days 21-30) | ✅ COMPLETE | Hierarchical indexing, MMR diversity, 7 components |

**Archival Reason**: Integration plans were detailed task breakdowns for implementation. All three phases have been completed successfully. These files are useful for understanding the implementation strategy and task dependencies.

---

## Archived Implementation Summaries

These documents track the completion of specific components and phases. They serve as historical records of implementation progress.

### Phase 1: PREMem Quality Assessment

| File | Date | Component | Status | LOC |
|------|------|------------|--------|-----|
| **PHASE1_PREMEM_IMPLEMENTATION_SUMMARY.md** | 2025-12-25 | QualityAssessor module | ✅ COMPLETE | 512 |
| **QUALITY_METRICS_IMPLEMENTATION_SUMMARY.md** | 2025-12-25 | MCP quality metrics tool | ✅ COMPLETE | 325 |

### Phase 2: GENESIS Capacity Management

| File | Date | Component | Status | LOC |
|------|------|------------|--------|-----|
| **PHASE2_TURSO_IMPLEMENTATION_SUMMARY.md** | 2025-12-25 | Turso storage backend | ✅ COMPLETE | 463 |
| **GENESIS_BENCHMARK_SUMMARY.md** | 2025-12-26 | Performance benchmarks | ✅ COMPLETE | 426 |

### Phase 3: Spatiotemporal Memory Organization

| File | Date | Component | Status | LOC |
|------|------|------------|--------|-----|
| **PHASE3_IMPLEMENTATION_SUMMARY.md** | 2025-12-26 | Phase 3 overall summary | ✅ COMPLETE | 505 |
| **DIVERSITY_MAXIMIZER_IMPLEMENTATION_SUMMARY.md** | 2025-12-26 | MMR algorithm implementation | ✅ COMPLETE | 546 |
| **PHASE3.1_COMPLETION_SUMMARY.md** | 2025-12-26 | Phase 3.1 core modules | ✅ COMPLETE | 489 |

### Consolidated Reports

| File | Date | Scope | Status | LOC |
|------|------|-------|--------|-----|
| **PHASES_1-3_IMPLEMENTATION_CONSOLIDATED.md** | 2025-12-28 | All phases 1-3 history | ✅ COMPLETE | 501 |
| **PHASE3_COMPLETION_CONSOLIDATED.md** | 2025-12-28 | Phase 3 completion tracking | ✅ COMPLETE | 361 |

### Research Analysis

| File | Date | Subject | Status | LOC |
|------|------|---------|--------|-----|
| **SPATIOTEMPORAL_INDEX_ANALYSIS.md** | 2025-12-26 | SpatiotemporalIndex integration analysis | ✅ COMPLETE | 679 |

### Final Reports

| File | Date | Subject | Status | LOC |
|------|------|---------|--------|-----|
| **FINAL_RESEARCH_INTEGRATION_REPORT.md** | 2025-12-27 | Complete 3-paper integration report | ✅ COMPLETE | 176 |
| **PHASE4_BENCHMARK_RESULTS.md** | 2025-12-26 | Phase 4 performance validation | ✅ COMPLETE | 348 |

**Archival Reason**: Implementation summaries document completed work. While valuable for historical tracking, they are not actively used for ongoing development. The final reports contain the most important findings.

---

## Research Categories

### Episodic Memory Research (COMPLETED - Q1 2026 Sprint)

**Papers Synthesized**:
- **PREMem** (EMNLP 2025): Pre-storage reasoning improves memory quality by 23%
- **GENESIS** (arXiv Oct 2025): Capacity-constrained encoding achieves 3.2x compression
- **Spatiotemporal** (arXiv Nov 2025): RAG enhancement improves retrieval by 34%

**Implementation Status**:
- ✅ PREMem quality assessment implemented (Phase 1)
- ✅ GENESIS capacity management implemented (Phase 2)
- ✅ Spatiotemporal organization implemented (Phase 3)
- ✅ All research claims validated (FINAL_RESEARCH_INTEGRATION_REPORT.md)

**Relevant Documents**:
- `EPISODIC_MEMORY_RESEARCH_2025.md` - Research synthesis (ACTIVE)
- `FINAL_RESEARCH_INTEGRATION_REPORT.md` - Implementation results (COMPLETE)

### Predictive Analytics Research

**Implemented Features**:
- ETS (Exponential Smoothing) forecasting: 20+ tests passing
- DBSCAN anomaly detection: 20+ tests passing
- BOCPD changepoint detection: 13+ tests passing

**Implementation**: Integrated and validated in do-memory-mcp

**Relevant Documents**:
- `ets_forecasting_best_practices.md` - ETS implementation guide (ACTIVE REFERENCE)
- `dbscan_anomaly_detection_best_practices.md` - DBSCAN implementation guide (ACTIVE REFERENCE)
- `current_implementation_analysis.md` - Implementation gap analysis (ACTIVE)

### Performance Benchmarking

**Benchmark Suite**:
- 6 comprehensive benchmark files
- Performance validation for all phases
- >100x faster than targets across most operations

**Relevant Documents**:
- `PERFORMANCE_BENCHMARKING_BEST_PRACTICES.md` - Benchmarking methodology (ACTIVE REFERENCE)
- `GENESIS_BENCHMARK_SUMMARY.md` - Phase 2 benchmarks (COMPLETE)
- `PHASE4_BENCHMARK_RESULTS.md` - Phase 4 validation (COMPLETE)

### MCP Protocol Research

**Research Focus**:
- MCP 2025-11-25 release analysis
- Backwards compatibility verification
- Async Tasks, OAuth 2.1, Extensions framework

**Relevant Documents**:
- `MCP_PROTOCOL_VERSION_RESEARCH.md` - Protocol update research (COMPLETE REFERENCE)

### Configuration Research

**Focus**: Configuration optimization and simplification (ARCHIVED)

**Key Findings** (from archive/research/):
- Configuration complexity was primary user adoption barrier
- Current implementation: 1480 LOC across 8 modules
- Target reduction: 80% (to ~300 LOC)
- Progress: 67% complete at time of research

**Relevant Documents** (in archive/research/):
- `CONFIG_ANALYSIS_AND_DESIGN.md`
- `CONFIG_ANALYSIS_SUMMARY.md`
- `comprehensive_configuration_lint_analysis.md`

---

## Research Impact Summary

### Completed Research (✅ Production Ready)
- ✅ PREMem quality assessment (Phase 1) - +23% memory quality
- ✅ GENESIS capacity management (Phase 2) - 5.56-30.6x compression
- ✅ Spatiotemporal retrieval (Phase 3) - +150% F1 improvement (4.4x better than target)
- ✅ Predictive analytics (ETS, DBSCAN, BOCPD) - 20+ tests passing each
- ✅ Performance benchmarking - All targets exceeded by 4-2307x
- ✅ MCP protocol research - Backwards compatible, async tasks identified

### Best Practices Documents (🟢 Active Reference)
- 🟢 ETS forecasting best practices (OxiDiviner)
- 🟢 DBSCAN anomaly detection best practices (linfa, dbscan, cogset)
- 🟢 Performance benchmarking best practices
- 🟢 MCP protocol version analysis

### Implementation Plans (📁 Archived - Completed)
- 📁 Phase 1 integration plan (26 atomic tasks, completed)
- 📁 Phase 2 integration plan (4 components, completed)
- 📁 Phase 3 integration plan (7 components, completed)

### Implementation Summaries (📁 Archived - Historical)
- 📁 15+ implementation summaries tracking progress
- 📁 Consolidated reports for phases 1-3
- 📁 Benchmark results and validation

---

## File Status Definitions

| Status | Meaning | Action |
|--------|---------|--------|
| **🟢 ACTIVE** | Currently relevant and in use | Keep in `plans/research/` |
| **🟢 REFERENCE** | Best practices or research used for reference | Keep in `plans/research/` |
| **✅ COMPLETE** | Implementation completed, documented | Archive (keep for historical reference) |
| **📁 ARCHIVED** | Historical record, not actively used | Archive to `plans/archive/` or keep in `plans/research/archive/` |
| **🔴 OBSOLETE** | Superseded by newer findings or no longer useful | Safe to delete |

---

## Recommended Actions

### 1. Keep in `plans/research/` (4 files - ACTIVE)
```
EPISODIC_MEMORY_RESEARCH_2025.md          # Research synthesis (current)
current_implementation_analysis.md           # Implementation analysis
ets_forecasting_best_practices.md           # ETS reference guide
dbscan_anomaly_detection_best_practices.md   # DBSCAN reference guide
PERFORMANCE_BENCHMARKING_BEST_PRACTICES.md # Benchmarking reference
MCP_PROTOCOL_VERSION_RESEARCH.md           # MCP protocol analysis
```

**Reason**: These documents contain current research findings and best practices that are actively referenced for ongoing work.

### 2. Archive to `plans/research/archive/` (19 files - COMPLETE)
Create subdirectory `plans/research/archive/` and move:

**Integration Plans** (3 files):
```
PHASE1_INTEGRATION_PLAN.md                # PREMem implementation plan
PHASE2_INTEGRATION_PLAN.md                # GENESIS implementation plan
PHASE3_INTEGRATION_PLAN.md                # Spatiotemporal implementation plan
```

**Implementation Summaries** (10 files):
```
PHASE1_PREMEM_IMPLEMENTATION_SUMMARY.md    # Phase 1 implementation
PHASE2_TURSO_IMPLEMENTATION_SUMMARY.md    # Turso storage implementation
PHASE3_IMPLEMENTATION_SUMMARY.md            # Phase 3 overall summary
DIVERSITY_MAXIMIZER_IMPLEMENTATION_SUMMARY.md  # MMR algorithm
PHASE3.1_COMPLETION_SUMMARY.md           # Phase 3.1 core modules
QUALITY_METRICS_IMPLEMENTATION_SUMMARY.md    # Quality metrics tool
PREMEM_PHASE1_IMPLEMENTATION_SUMMARY.md    # Duplicate of PHASE1_PREMEM
```

**Consolidated Reports** (3 files):
```
PHASES_1-3_IMPLEMENTATION_CONSOLIDATED.md # All phases history
PHASE3_COMPLETION_CONSOLIDATED.md        # Phase 3 completion tracking
```

**Research Analysis** (1 file):
```
SPATIOTEMPORAL_INDEX_ANALYSIS.md          # SpatiotemporalIndex analysis
```

**Final Reports** (2 files):
```
FINAL_RESEARCH_INTEGRATION_REPORT.md         # Complete integration results
PHASE4_BENCHMARK_RESULTS.md                # Phase 4 performance validation
```

**Reason**: These files document completed work and serve as historical records. They are not actively used for ongoing development but may be useful for understanding implementation history.

### 3. Delete (1 file - OBSOLETE DUPLICATE)
```
plans/research/SPATIOTEMPORAL_INDEX_ANALYSIS.md
```

**Reason**: This file analyzes whether to integrate or remove the SpatiotemporalIndex. The analysis concluded that the index should be **integrated**, not removed. Since the integration work is now complete (documented in PHASE3_IMPLEMENTATION_SUMMARY.md and FINAL_RESEARCH_INTEGRATION_REPORT.md), this analysis document is no longer needed and would be confusing if kept.

### 4. Update `RESEARCH_INDEX.md`
This file (the one you're reading) is the updated index reflecting the current state of research documentation.

---

## Archive Directory Structure

After archiving, the structure should be:

```
plans/
├── RESEARCH_INDEX.md                       # This file (updated)
└── research/
    ├── ACTIVE/                              # Current research
    │   ├── EPISODIC_MEMORY_RESEARCH_2025.md
    │   ├── current_implementation_analysis.md
    │   ├── ets_forecasting_best_practices.md
    │   ├── dbscan_anomaly_detection_best_practices.md
    │   ├── PERFORMANCE_BENCHMARKING_BEST_PRACTICES.md
    │   └── MCP_PROTOCOL_VERSION_RESEARCH.md
    └── archive/                              # Historical records
        ├── integration_plans/
        │   ├── PHASE1_INTEGRATION_PLAN.md
        │   ├── PHASE2_INTEGRATION_PLAN.md
        │   └── PHASE3_INTEGRATION_PLAN.md
        ├── implementation_summaries/
        │   ├── PHASE1_PREMEM_IMPLEMENTATION_SUMMARY.md
        │   ├── QUALITY_METRICS_IMPLEMENTATION_SUMMARY.md
        │   ├── PHASE2_TURSO_IMPLEMENTATION_SUMMARY.md
        │   ├── GENESIS_BENCHMARK_SUMMARY.md
        │   ├── DIVERSITY_MAXIMIZER_IMPLEMENTATION_SUMMARY.md
        │   ├── PHASE3_IMPLEMENTATION_SUMMARY.md
        │   ├── PHASE3.1_COMPLETION_SUMMARY.md
        │   └── PREMEM_PHASE1_IMPLEMENTATION_SUMMARY.md (DUPLICATE)
        ├── consolidated_reports/
        │   ├── PHASES_1-3_IMPLEMENTATION_CONSOLIDATED.md
        │   ├── PHASE3_COMPLETION_CONSOLIDATED.md
        │   ├── FINAL_RESEARCH_INTEGRATION_REPORT.md
        │   └── PHASE4_BENCHMARK_RESULTS.md
        └── analysis/
            └── SPATIOTEMPORAL_INDEX_ANALYSIS.md
```

---

## Research Methodology

### Multi-Agent Analysis Framework
1. **Code Reviewer**: Quality assessment, best practices compliance
2. **Feature Implementer**: Implementation feasibility, effort estimation
3. **Refactorer**: Code complexity analysis, optimization opportunities
4. **Analysis Swarm**: Cross-domain insights, trade-off analysis

### Documentation Standards
- Comprehensive findings with evidence
- Actionable recommendations with priorities
- Code references with file:line format
- Success criteria and validation metrics

### Review Cycle
- **Weekly**: Active research updates (when applicable)
- **Monthly**: Research summary and archival
- **Quarterly**: Research strategy review (Q1 sprint kickoff: 2026-01-25)

---

## Access Guidelines

### For Current Research
Check `plans/research/ACTIVE/` for ongoing investigations and implementation analysis.

### For Best Practices
Review reference documents in `plans/research/ACTIVE/`:
- ETS and DBSCAN documents for algorithm implementation patterns
- Performance benchmarking guide for benchmark methodology
- MCP protocol research for server updates

### For Historical Research
Check `plans/research/archive/` for:
- Completed implementation plans (understanding task breakdown)
- Implementation summaries (historical progress tracking)
- Consolidated reports (overall project status)
- Final validation results (performance claims)

### For Configuration Research
Check `archive/research/` (parent directory) for:
- Configuration optimization work (completed 2025-12-20)
- System architecture analysis

---

## Research Quality Metrics

| Metric | Target | Current | Status |
|--------|--------|---------|--------|
| **Evidence-Based** | 100% | 100% | ✅ |
| **Actionable Recommendations** | 100% | 100% | ✅ |
| **Code References** | >50% | 85% | ✅ |
| **Validation Metrics** | 100% | 100% | ✅ |
| **Multi-Source** | >2 sources | 3+ | ✅ |

---

## Summary Statistics

### Current State
- **Active Research Files**: 6 files (~4,300 LOC)
- **Archived Files**: 19 files (~6,900 LOC)
- **Reduction**: 76% reduction in active files (from 25 to 6)

### Research Coverage
- **3 Academic Papers Synthesized**: PREMem, GENESIS, Spatiotemporal
- **3 Implementation Phases**: Quality Assessment, Capacity Management, Retrieval Optimization
- **2 Best Practice Guides**: ETS Forecasting, DBSCAN Anomaly Detection
- **1 Performance Methodology**: Comprehensive benchmarking
- **1 Protocol Analysis**: MCP 2025-11-25

### Implementation Status
- **Phase 1 (PREMem)**: ✅ Complete (89% quality accuracy)
- **Phase 2 (GENESIS)**: ✅ Complete (5.56-30.6x compression)
- **Phase 3 (Spatiotemporal)**: ✅ Complete (+150% F1 improvement)
- **Phase 4 (Benchmarks)**: ✅ Complete (all claims validated)

---

**Last Updated**: 2025-12-27
**Next Review**: 2026-01-25 (monthly research cycle, Q1 sprint kickoff)
**Maintainer**: Research team and technical documentation

---

*This index provides a comprehensive, organized view of all research documentation, distinguishing between active reference materials and archived implementation records.*
