Quantum PCA for Gene-Expression Data — 2D Rotatable Projection

Gene-Expression Cohort

Correlation ρ across genes 0.60

Cohort size N 160

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Classical PCA (power iteration)

λ₁ (PC1)

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λ₂ (PC2)

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λ₃ (PC3)

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PC1 variance

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Quantum Phase Estimation on ρ

Ancilla (precision) qubits t 4

φ target = 0.000 → estimate = 0.000

Classical reads

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Quantum qubits

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How it works

Each point is a "sample" in a 3-gene expression space, drawn from a Gaussian with a tunable pairwise correlation ρ (Cholesky-factored so the target covariance is exact). Classically, PCA power-iterates the empirical covariance matrix C = (1/N)Σ(xᵢ−x̄)(xᵢ−x̄)ᵀ:

v ← Cv / |Cv|,  λ ← vᵀCv   (repeat to converge, then deflate and repeat)

The rods drawn through the rotatable point cloud are the converged eigenvectors, scaled by √λ. Quantum PCA instead treats the normalized covariance matrix as a density operator ρ = C/tr(C) and exponentiates many copies of ρ to synthesize e^(−iρt); running Quantum Phase Estimation (QPE) on that unitary extracts each eigenvalue λ using only t = O(log(1/ε)) ancilla qubits, versus reading every one of the d² classical matrix entries.

The histogram panel is the exact QPE outcome distribution for measuring the top eigenvalue's phase φ = λ₁ / (2·tr C) with t ancilla qubits — the real Nielsen–Chuang result, not a mock-up:

P(y) = sin²(π(2ᵗφ − y)) / (2²ᵗ · sin²(π(φ − y/2ᵗ)))

Raise t and watch the peak sharpen around the true phase: that narrowing is the source of QPCA's claimed exponential advantage for high-dimensional genomic covariance matrices — at the cost of needing coherent access to many copies of the quantum state, which is why it remains a NISQ-era research idea rather than a deployed bioinformatics tool.

Expression samples Principal axes (√λ scaled)

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