QuantumGenome EDS Discovery Engine

QuantumGenome EDS is a real-data genomics discovery project that converts variant data into an Ising-style interaction model and uses QAOA-based search to identify low-energy, disease-loaded multi-variant patterns.

The project began as a quantum-assisted Ehlers-Danlos / collagen discovery pipeline built from ClinVar and later expanded into a Jetson-first local discovery framework with same-gene, same-disease, position-window, mixed-biologic, novel-candidate, and epistasis-hypothesis phases.

Real Results Achieved

This project has documented end-to-end validation on real data.

• Parsed 4,129,628 ClinVar variants and built disease-specific EDS and collagen panels.
• Validated h[i] scoring from ClinVar significance and J[i,j] scoring from shared disease annotations.
• In a PLOD1 baseline run, the lowest-energy bitstring was 0001 at -5.0, correctly isolating the disease-driving variant.
• In a B3GALT6 EDS cluster run, four pathogenic / likely pathogenic variants sharing spondylodysplastic EDS annotation produced pairwise J[i,j] = +1.2 and a lowest-energy bitstring of 1101 at -4.0.
• In a 1000 Genomes chr22 pilot, the full real-data loop was validated: genotype matrix -> h/J -> classical energy spectrum -> QAOA simulator -> measured bitstrings.

What Is In This Public Repo

This public repo includes runnable Python scripts with placeholder IBM settings so another user can:

1. copy config_template.py to config.py
2. enter their own IBM credentials and backend
3. run the ETL / panel / QAOA workflow themselves

IBM Quantum Support In This Repo

The file quantum_model_builder.py includes:

• local Aer simulator mode
• IBM Quantum submission mode through QiskitRuntimeService
• placeholder settings in config_template.py
• USE_IBM = False by default for safe first runs

To use IBM Quantum:

1. copy config_template.py to config.py
2. fill in your own IBM_TOKEN, IBM_INSTANCE, and IBM_BACKEND
3. set USE_IBM = True in quantum_model_builder.py
4. run python3 quantum_model_builder.py

Public / Private Boundary

This repository is publicly visible for portfolio, review, and discussion purposes only. All rights are reserved by the author unless explicit written permission is granted. No open-source license is provided for this repository.