HomeHeroesDe NovoDiscoveryGene ScanCDx Pathwayโ™ป๏ธ Repurposing๐Ÿšฆ GatesModelsQuantum๐Ÿงช Wet LabSchedules๐ŸŽ›๏ธ Control๐Ÿงฌ CIFOG๐Ÿ“ˆ Milestones๐Ÿงฌ BioBrain๐Ÿง  NPEADArchitecture๐Ÿ”ฌ RODE๐Ÿง  Cortex-RWorkspace๐Ÿง  V2๐Ÿง  V3๐Ÿ“ฆ Knowledge๐Ÿ’ฐ Revenue๐Ÿงช Tests๐Ÿ“Š Costs๐Ÿ“š Datasets

๐Ÿง  Cortex Autonomous Intelligence

Cortex is a self-improving scientific reasoning engine โ€” it scores, learns, teaches itself, reasons about repurposing, and gates its own compute authority. All decisions governed and hash-chained.

Cortex Capability Status (Live)

โ— 16-Brain Fusion โ€” Genomics, Transcriptomics, Pathway, GCN, Chemistry, Clinical, Biomarker, DepMap, PubMed, Cancer, Competitor, Curiosity, Quantum, Evidence, NPEAD, Proteomics
โ— Online Learning โ€” Learns from every outcome (corrections applied to weights each run)
โ— GCN Self-Teaching โ€” Graph neural network trains on CIFOG nodes โ†’ writes signals back to brains
โ— Teacher (Claude Opus 4.8) โ€” Evaluates brain quality, generates weight corrections nightly
โ— Repurpose-First Reasoning โ€” Checks existing drugs before de novo generation
โ— Quantum Meta-Learning โ€” VQE search proposals for ambiguous scoring cases
โ— Real Omics Refresh โ€” 441 signals from TCGA (4 cancers) refreshed each run
โ— Autonomous Discovery โ€” Promotes high-scoring genes to heroes without human input
โ— Evidence Hash Chain โ€” Every decision SHA-256 linked, S3 immutable ledger
โ— Authority Gating (PQM) โ€” Self-checks permission before acting
โ— S3 Weight Backup + Snapshots โ€” Full state reproducibility per run
โ— Gene Discovery Scan โ€” Queues novel candidates from platform state
โ— Active Learning (SMARTER_COMPOUNDS) โ€” MD survivors bias next-gen molecules
โ— Preliminary Quality Gate โ€” Druggability scoring before GPU spend
โ— Brain Disagreement Surfacing โ€” 5-brain quorum voting, conflict detection, severity scoring
โ— NPEAD v2 (6-Axis) โ€” TV, SV, UR, F, S, EC + Default/Hypothesis/Exploration modes
โ— BioBrain Phase 1 โ€” SafetyNet + SynthNet + BindNet + PocketNet + Orchestrator
โ— BrainSignal Reasoning โ€” Structured "why" field per gene (Level 4 foundation)
โ— Discovery Outcome Recording โ€” Failure reasons + scaffold stats + generator version
โ— Decision Comparison (v1/v2) โ€” A/B framework ready, awaiting hypothesis engine
โ—‹ Hypothesis Generation โ€” Proposes "test X because Y" (Level 4, 3 days)
โ—‹ Biological World Model โ€” Causal graph of mechanisms (Level 5, 7 days)

โ— Live (18)   โ— Deployed, accumulating (4)   โ—‹ Specified (2)

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๐Ÿ’ฐ Revenue๐Ÿ“Š Costs๐Ÿ“š Datasets

๐ŸŽฏ Experiment Priority Queue

Ranked by information gain per dollar. Cortex decides what to run next. ๐Ÿ“„ Full Experiment Report (PDF)

๐Ÿ“ˆ Cortex Scientific Activity (updates every run)

๐Ÿง  Teacher Activity (Opus 4.8 evaluations)

#GeneExperimentPriorityInfo GainCostReasoning

๐Ÿงช Wet Lab Orders

Synthesis orders + assay protocols for A/A+ compounds. Pending governance approval.

GeneCompoundStatusCostTimelineHash

๐Ÿ”— Cross-Target Combinations

Pathway convergence โ†’ combination hypotheses.

๐Ÿ’ฐ Revenue๐Ÿ“Š Costs๐Ÿ“š Datasets

โŒ Failure Taxonomy

Structured failure memory โ€” avoidance rules prevent repeating mistakes.

CategoryCountPatternAvoidance Rule

๐Ÿ“š External Validation

Papers vs our predictions โ€” auto-confidence updates.

๐Ÿ’ฐ Revenue๐Ÿ“Š Costs๐Ÿ“š Datasets

๐Ÿ”’ Governance Ledger

Every decision hash-chained to immutable S3 ledger.

๐Ÿ’ฐ Revenue๐Ÿ“Š Costs๐Ÿ“š Datasets