# Graph Report - .  (2026-06-13)

## Corpus Check
- Corpus is ~2,339 words - fits in a single context window. You may not need a graph.

## Summary
- 61 nodes · 78 edges · 9 communities (5 shown, 4 thin omitted)
- Extraction: 88% EXTRACTED · 12% INFERRED · 0% AMBIGUOUS · INFERRED: 9 edges (avg confidence: 0.76)
- Token cost: 49,231 input · 0 output

## Community Hubs (Navigation)
- [[_COMMUNITY_Second Brain Workspace and Tooling|Second Brain Workspace and Tooling]]
- [[_COMMUNITY_Core LLM Research Papers|Core LLM Research Papers]]
- [[_COMMUNITY_Reasoning and Agent Concepts|Reasoning and Agent Concepts]]
- [[_COMMUNITY_Attention Efficiency and Long Context|Attention Efficiency and Long Context]]
- [[_COMMUNITY_Workspace Hard Rules|Workspace Hard Rules]]
- [[_COMMUNITY_GPT-1 Pre-Training|GPT-1 Pre-Training]]
- [[_COMMUNITY_Literature Review Draft|Literature Review Draft]]
- [[_COMMUNITY_Inbox Folder|Inbox Folder]]
- [[_COMMUNITY_Sources Folder|Sources Folder]]

## God Nodes (most connected - your core abstractions)
1. `/graphify Command` - 8 edges
2. `Workspace Hard Rules` - 8 edges
3. `Research Second Brain Starter Workspace` - 6 edges
4. `graphify-out/ Folder` - 6 edges
5. `Research Second Brain Workspace Rules` - 6 edges
6. `Chain-of-Thought Prompting` - 5 edges
7. `Chain-of-Thought (CoT) Prompting` - 5 edges
8. `ReAct: Interleaved Reasoning Traces and Actions` - 5 edges
9. `inbox/ Folder` - 5 edges
10. `/setup-check Command` - 5 edges

## Surprising Connections (you probably didn't know these)
- `Self-Supervised Tool Use Learning` --semantically_similar_to--> `ReAct: Interleaved Reasoning Traces and Actions`  [INFERRED] [semantically similar]
  sources/corpus-pdfs/2023_toolformer_2302.04761.pdf → sources/corpus-pdfs/2022_react_2210.03629.pdf
- `Research Second Brain Workspace Rules` --references--> `Research Second Brain Starter Workspace`  [INFERRED]
  AGENTS.md → README.md
- `Research Second Brain Workspace Rules` --references--> `sources/ Folder`  [EXTRACTED]
  AGENTS.md → README.md
- `Graphify CLI (pinned class-tested version)` --references--> `/graphify Command`  [EXTRACTED]
  AGENTS.md → README.md
- `/setup-check Command` --references--> `Graphify CLI (pinned class-tested version)`  [EXTRACTED]
  README.md → AGENTS.md

## Hyperedges (group relationships)
- **LLM Reasoning Capability Progression** — paper_wei2022cot, paper_yao2023tot, paper_yao2022react, rationale_chain_of_thought, rationale_emergent_ability_scale [EXTRACTED 0.95]
- **Attention Mechanism Efficiency Lineage** — paper_shazeer2019mqa, paper_ainslie2023gqa, paper_munkhdalai2024infini, paper_qwen2024, rationale_kv_cache_efficiency [EXTRACTED 0.90]
- **LLM Agency Tool Use and Alignment** — paper_schick2023toolformer, paper_yao2022react, paper_bai2022cai, paper_radford2018gpt1, rationale_tool_use_self_supervised [EXTRACTED 0.85]
- **Second Brain Loop: inbox to /graphify to graphify-out** — readme_inbox_folder, readme_graphify_command, readme_graphify_out_folder, readme_second_brain_workflow [EXTRACTED 1.00]
- **Researcher Judgment Protection Rules** — agents_never_guess_metadata_rule, agents_judgment_fields_human_rule, agents_paper_separate_from_reader_rule, agents_preserve_source_context_rule [INFERRED 0.85]
- **Workspace Folder Structure** — readme_inbox_folder, readme_sources_folder, readme_graphify_out_folder, readme_fallback_folder, readme_claude_folder [EXTRACTED 1.00]

## Communities (9 total, 4 thin omitted)

### Community 0 - "Second Brain Workspace and Tooling"
Cohesion: 0.26
Nodes (15): Graphify CLI (pinned class-tested version), Inbox First Rule, Research Second Brain Workspace Rules, .claude/ Tooling Folder, Demo Notes (LLM/AI-agent research corpus), fallback/ Folder (pre-built graph), Graph Artifacts (graph.html, GRAPH_REPORT.md, graph.json), /graphify Command (+7 more)

### Community 1 - "Core LLM Research Papers"
Cohesion: 0.24
Nodes (12): Constitutional AI: Harmlessness from AI Feedback, Toolformer: Language Models Can Teach Themselves to Use Tools, Chain-of-Thought Prompting Elicits Reasoning in LLMs, ReAct: Synergizing Reasoning and Acting in Language Models, Tree of Thoughts: Deliberate Problem Solving with LLMs, Chain-of-Thought (CoT) Prompting, Constitutional AI and RLAIF, Emergent Abilities at Scale (+4 more)

### Community 2 - "Reasoning and Agent Concepts"
Cohesion: 0.18
Nodes (12): Chain-of-Thought Prompting, CoT as Emergent Ability of Scale, Cross-Episode Agent Memory Gap, ReAct Loop Thought-Action-Observation, Reflexion Verbal Reinforcement Learning, Self-Consistency Decoding, Toolformer Self-Supervised Tool Learning, Tree of Thoughts Search (+4 more)

### Community 3 - "Attention Efficiency and Long Context"
Cohesion: 0.24
Nodes (10): GQA: Training Generalized Multi-Query Transformer Models, Leave No Context Behind: Infini-attention, Qwen2 Technical Report, Fast Transformer Decoding: Multi-Query Attention, Grouped-Query Attention (GQA), Infini-Attention: Compressive Memory + Local Attention, KV Cache Efficiency for LLM Inference, LLM Alignment via RLHF (+2 more)

### Community 4 - "Workspace Hard Rules"
Cohesion: 0.38
Nodes (7): Workspace Hard Rules, Judgment Fields Are Human Rule, Never Guess Metadata Rule (TODO-VERIFY), One Step At A Time Rule, Keep Paper Separate From Reader Rule, Preserve Source Context Rule, Show Your Work Rule

## Knowledge Gaps
- **17 isolated node(s):** `Toolformer Notes Schick 2023`, `Lit Review Draft Fragment Reasoning Methods`, `Inbox Folder README`, `Self-Consistency Decoding`, `Reading Notes 2025 Tree of Thoughts Reflexion` (+12 more)
  These have ≤1 connection - possible missing edges or undocumented components.
- **4 thin communities (<3 nodes) omitted from report** — run `graphify query` to explore isolated nodes.

## Suggested Questions
_Questions this graph is uniquely positioned to answer:_

- **Why does `Constitutional AI and RLAIF` connect `Core LLM Research Papers` to `Attention Efficiency and Long Context`?**
  _High betweenness centrality (0.063) - this node is a cross-community bridge._
- **Why does `LLM Alignment via RLHF` connect `Attention Efficiency and Long Context` to `Core LLM Research Papers`?**
  _High betweenness centrality (0.061) - this node is a cross-community bridge._
- **Why does `Workspace Hard Rules` connect `Workspace Hard Rules` to `Second Brain Workspace and Tooling`?**
  _High betweenness centrality (0.059) - this node is a cross-community bridge._
- **What connects `Toolformer Notes Schick 2023`, `Lit Review Draft Fragment Reasoning Methods`, `Inbox Folder README` to the rest of the system?**
  _17 weakly-connected nodes found - possible documentation gaps or missing edges._