🧬 CIFOG — Cortex Integrated Fused Omics Graph
Governed · Sharded · Vector-Native · GCN Classical+Quantum · Distributed to Edge
Core Innovation: Not a knowledge graph with omics layers. An omics-fused graph where integration IS the structure. Every node is a fused multi-omics state. GCN (classical + quantum) learns patterns across the graph. Biologically sharded by cancer type, distributed to edge principals via governed leases.
Real Docking Integration: Uni-Dock GPU docking scores now feed directly into the CIFOG graph. Docking affinity and pose quality become node features, enabling the GCN to learn binding-informed patterns across cancer shards.
Philosophy
We don't store what the world knows. We build what we need to know, at the moment we need to know it, with expert precision — then distill and propagate only what has been validated by real outcomes.
Knowledge is constructed, perishable, and earned — not stored, static, and retrieved.
| Principle | Meaning |
|---|
| Just-in-time construction | Knowledge built on demand, not pre-loaded |
| Multi-omics fusion at the node | Integration IS the structure, not a query-time join |
| Skill acquisition | Learn decision patterns, not entity relationships |
| Outcome validation | Knowledge earns authority only through confirmed predictions |
| Temporal decay | Unvalidated knowledge loses authority automatically |
| Governed propagation | Distilled knowledge flows only to authorized principals |
Architecture
┌─────────────────────────────────────────────────────────────────┐
│ CORTEX INTEGRATED FUSED OMICS GRAPH (CIFOG) │
│ │
│ ┌───────────────────────────────────────────────────────────┐ │
│ │ FUSED NODES │ │
│ │ │ │
│ │ KRAS:PAAD ─── BRAF:PAAD ─── MEK1:PAAD ─── ERK2:PAAD │ │
│ │ │ │ │ │ │
│ │ Each node = genomic + transcriptomic + proteomic + │ │
│ │ pathway + clinical (ALL FUSED AT WRITE TIME) │ │
│ │ │ │
│ │ Edges = cross-modal interactions (not single-modality) │ │
│ └───────────────────────────────────────────────────────────┘ │
│ │ │
│ ┌───────────────┼───────────────┐ │
│ ▼ ▼ │
│ ┌─────────────────────┐ ┌─────────────────────────┐ │
│ │ CLASSICAL GCN │ │ QUANTUM GCN │ │
│ │ │ │ │ │
│ │ 3 conv layers │ │ Amplitude encoding │ │
│ │ 64→128→256 filters │ │ Edge entanglement │ │
│ │ Learns motifs from │ │ Variational ansatz │ │
│ │ EGAO outcomes │ │ Braket SV1 / IonQ │ │
│ │ │ │ │ │
│ │ Routine: <50ms │ │ Discovery: <30s │ │
│ │ 90% of queries │ │ When classical < 0.5 │ │
│ └──────────┬──────────┘ └────────────┬────────────┘ │
│ └──────────────┬────────────────┘ │
│ ▼ │
│ ┌───────────────────────────────────────────────────────────┐ │
│ │ AUTHORITY GATE │ │
│ │ GCN confidence → authority score → EXECUTE or STOP │ │
│ │ Evidence: which conv filters fired = explanation │ │
│ └───────────────────────────────────────────────────────────┘ │
└─────────────────────────────────────────────────────────────────┘
│ │
▼ ▼
┌─────────────────┐ ┌─────────────────┐
│ Edge Node A │ │ Edge Node B │
│ (hospital) │ │ (pharma lab) │
│ PAAD shard │ │ BRCA+LUAD │
│ ~50 nodes │ │ ~100 nodes │
│ (lease-scoped) │ │ (lease-scoped) │
└─────────────────┘ └─────────────────┘
Fused Node
The fundamental unit. Not an entity with typed edges — a single fused multi-omics state:
Traditional BKG:
KRAS (Gene) ──[has_mutation]──▶ G12C (Variant)
KRAS (Gene) ──[expressed_in]──▶ PAAD (Cancer)
KRAS (Gene) ──[member_of]──▶ MAPK (Pathway)
KRAS (Gene) ──[targeted_by]──▶ Sotorasib (Drug)
→ 4 separate facts, no integration
CIFOG Fused Node:
KRAS:PAAD {
genomic: {mutation: G12C, frequency: 0.92, CNV: neutral, MSI: stable}
transcriptomic: {expression_z: 2.4, splicing: canonical}
proteomic: {abundance: high, phospho: active, localization: membrane}
pathway: {MAPK: active, PI3K: co-active, centrality: 0.89}
clinical: {sotorasib: approved, resistance: NRAS_amp(0.3)}
classification: DRIVER
actionability: 0.94
authority: 0.91
}
→ One integrated truth, all modalities simultaneous
GCN: Classical + Quantum
| Property | Classical GCN | Quantum GCN (QGCN) |
|---|
| Purpose | Routine inference | Discovery + contradiction resolution |
| Speed | <50ms per node | <30s per node |
| Trigger | Every query | Classical confidence < 0.5 |
| Architecture | 3 conv layers (64→128→256) | Amplitude encode + edge entangle + variational |
| Learns | Neighborhood motifs from outcomes | Multi-body interactions (3+ nodes) |
| Discovers | Known pattern recognition | Novel edges invisible to classical |
| Cost | ~$0 (CPU) | ~$0.30-5 (Braket/IonQ) |
| Governance | Standard authority gate | PQM-governed escalation |
| Training | EGAO outcomes (weekly retrain) | Hybrid classical-quantum loop |
Classical GCN confidence ≥ 0.5 → USE RESULT (governed output)
Classical GCN confidence < 0.5 → ESCALATE TO QUANTUM GCN
→ PQM authorizes spend
→ QGCN runs on Braket
→ Validate result classically
→ USE RESULT (higher authority if validated)
Sharding
Primary Shards (by cancer type):
cifog-paad → Pancreatic (~500 fused nodes)
cifog-brca → Breast (~600 fused nodes)
cifog-luad → Lung (~450 fused nodes)
cifog-prad → Prostate (~400 fused nodes)
Cross-Shard Index (pan-cancer):
cifog-global → Nodes in ≥3 shards (TP53, KRAS, PIK3CA...)
Pathway Sub-Shards:
cifog-paad:mapk → MAPK cascade nodes
cifog-paad:pi3k → PI3K/AKT/mTOR nodes
cifog-paad:chromatin → Chromatin remodeling nodes
Edge Distribution
| Principal | Receives | Nodes | Lease |
|---|
| Hospital oncology | cifog-paad (full shard) + global top-50 | ~550 | 30 days |
| Pharma KRAS program | cifog-paad:mapk + cifog-luad:mapk + global:KRAS | ~200 | 90 days |
| Broad discovery | cifog-global + top-authority per shard | ~300 | 14 days |
Knowledge Lifecycle
CONSTRUCT → VALIDATE → COMPRESS → PROPAGATE → DECAY → RE-LEARN
┌──────────────────────────────────────────────────────────────┐
│ Authority ≥ 0.7: USE STORED (recall, <50ms) │
│ 0.4 < Auth < 0.7: REFRESH (update stale modalities) │
│ Authority < 0.4: CONSTRUCT FROM SCRATCH (JIT, <30s) │
└──────────────────────────────────────────────────────────────┘
Validation: Outcome confirms → authority +0.05
Outcome contradicts → authority -0.10
Decay: No validation in 60 days → authority drops
Propagation: Authority ≥ 0.75 + 3 validations → push to edge
vs Competition
| WBKG / Neo4j Graph RAG | CIFOG |
|---|
| Structure | Entity-relationship (separate layers) | Fused omics vectors (integration IS the node) |
| ML Algorithm | k-NN / retrieval | GCN classical + quantum |
| Storage | Centralized Neo4j | Sharded vectors, distributed to edge |
| Learning | None (static load) | Online from outcomes + quantum discovery |
| Governance | None | Authority-gated, hash-chained, lease-scoped |
| Temporal | Snapshot (stale) | Continuous decay + re-validation |
| Edge/Offline | Cloud-only | Shard subsets propagate, work offline |
| Output | "Here are related entities" | "Here's what to do, with this confidence" |
Implementation Roadmap
| Phase | Scope | Timeline | Status |
|---|
| 1 | Data model + sharding + prior knowledge loader | Weeks 1-3 | Planned |
| 2 | JIT fused node construction engine | Weeks 4-6 | Planned |
| 3 | Classical GCN training + inference integration | Weeks 7-9 | Planned |
| 4 | Quantum GCN + edge discovery | Weeks 10-12 | Planned |
| 5 | Distillation + propagation + Edge SDK | Weeks 13-15 | Planned |
| 6 | Production hardening | Weeks 16-18 | Planned |
Patent Position
Extends Patent Family 64/036,705 (EGAO):
- Fused omics nodes as structural integration (not query-time join)
- GCN classical+quantum dual-substrate learning on biomedical graph
- Biologically-sharded governed graph with lease-scoped propagation
- JIT knowledge construction under authority governance
- Temporal authority decay on fused state
- Quantum edge discovery in multi-modal interaction space
→ Full Architecture🔬 RODE🧠 Cortex-R · → Quantum · → Multi-Omics · → Models
CIFOG — Cortex Integrated Fused Omics Graph | May 2026