created: 20260506130000000
modified: 20260526190000000
tags: ResearchStack Home
title: Research Stack Home
type: text/vnd.tiddlywiki

! Research Stack Local TiddlyWiki

This is the local nonlinear note surface for the Research Stack.
Use it for fast concept cards, cross-links between ideas and formal surfaces,
and temporary maps before promotion into the durable doc layer.

!! Architecture & Infrastructure

* [[Research Stack Architecture]] — 6-layer system overview
* [[ENe Cognitive Refactor Plan]] — 14-week infrastructure roadmap
* [[ENE API Hook]] — AES-256-GCM encryption + secure storage
* [[Swarm ENE Middleware]] — query caching + audit + semantic search
* [[ENE Wiki Layer]] — revisioned wiki with 14D concept vectors
* [[TiddlyWiki ENE Bridge Plugin]] — wiki-to-swarm bridge

!! Compression Pipeline

* [[Hutter Prize Compression]] — enwik9 static target
* [[Hutter Prize ISA]] — compression-optimized instruction set
* [[Hutter Critical Analysis]] — claim-boundary audit rail
* [[Delta GCL Compression]] — Metafoam → GCL → AES pipeline
* [[GCL Nanokernel]] — self-hosting compression execution
* [[Compression and Soliton Mining]] — compression discovery
* [[Engram Decompressor]] — decode path

!! Lean Formal Verification

* [[PIST Route-Repair and Receipt Update]] — v1.4/v1.4a repair status, Q16.16 quaternion receipts, and genus-0 control correction
* [[Lean Semantics Overview]] — 421 .lean files, 31 subdirectories
* [[Fixed Point Algebra]] — Q16_16 arithmetic proofs
* [[Mass Number Theory]] — admissibility gate (A ≤ τ·(R + ε))
* [[Sigma Gate]] — entropy-based operation gating
* [[Yang-Mills Compression]] — gauge-theoretic encoding bounds
* [[PIST Shell Encoding]] — (k, t) coordinate system
* [[FiveD Torus Topology]] — periodic boundary routing
* [[AVMR Adaptive Vector Manifold Representation]] — 7-module framework
* [[AMMR Adaptive Meshless Methods]] — mesh-free PDE solving

!! Topology, TSM & Manifolds

* [[Topological State Machine]] — geometric state evolution
* [[Manifold Flow]] — gradient descent on manifold surfaces
* [[Semantic RG Flow]] — scale-invariant semantic operations
* [[Unified Hypersurface]] — multi-manifold computation
* [[Menger Sponge Fractal Addressing]] — void-based routing
* [[FAMM Fast Approximate Manifold Map]] — binary state cache
* [[Waveprobe]] — manifold probing + wavefront propagation
* [[Semantic Eigenvector Bundle]] — equation→eigenvector mapping
* [[Equation Forest Index]] — structured equation catalog

!! Pathological Manifolds (CAD)

* [[Pathological Manifold Torus]] — 3D hypertorus slice
* [[Pathological Menger-Horn Composite]] — sponge on horn
* [[Pathological PIST Shells]] — concentric shell rings
* [[Manifold Viewer]] — WebGL 3D visualizations

!! Search & Graph Mining

* [[HNSW Vector Search]] — O(log N) ANN over concept vectors
* [[Semantic Graph Mining]] — graph extraction + community detection
* [[Graph-Evolving RAG]] — retrieval-augmented generation
* [[Internal Semantic Search]] — local search surface
* [[Address-First Search Protocol]] — coordinate-prior search
* [[Erdos Four Primitive Diagnostics]] — conjecture-test packets, detector anomalies, and receipt gates

!! Biology & Genetics

* [[Genetic Code Pipeline]] — codon→gene→chromosome→genome
* [[Hachimoji Pipeline]] — 8-letter genetic alphabet
* [[Synthetic Genetic Coding]] — DNA as programmable storage
* [[Peptide MoE]] — mixture-of-experts for peptides
* [[Extremophile Constraint Layer]] — 4Gyr survival bounds
* [[RNA to Peptide Shifter]] — ribosomal encoding

!! Hardware & GPU

* [[FPGA Warden]] — hardware security + compute offload
* [[ASIC Topology]] — topological die layout
* [[HDMI Compute Fabric]] — display-as-compute
* [[Morphic DSP]] — reconfigurable signal processing
* [[Virtual Display Blitter Compute Surface]] — WGSL rendering

!! Data & Ingestion

* [[Data Ingestion Pipeline]] — multi-source knowledge feed
* [[Mined Conversation Concepts]] — mined concept index
* [[Conversation Mining Source Map]] — source tracking
* [[Full Chat Log Dumps]] — raw conversation archives
* [[Speculative Materials]] — hypothesis sandbox

!! Concepts & Tools

* [[Concept Vector 14]] — 14D semantic vector spec
* [[Semantic Prime Refraction]] — prime-based concept routing
* [[Golden Angle Encoding]] — φ-irrational rotations
* [[Gray-Code Golden-Spiral Fold]] — spiral compression
* [[COUCH Family]] — constraint unification
* [[Monster Filter Family]] — anomaly detection
* [[Triumvirate Enforcer]] — 3-party consensus

!! Durable Markdown Surfaces

* `../wiki/Home.md`
* `../wiki/Glossary.md`
* `../wiki/Concept-Archive.md`
* `../docs/GLOSSARY.md`
* `../docs/WEIRD_CONCEPTS_GLOSSARY.md`