Current single-cell clustering pipelines discard most genes and can yield inconsistent clusters across random seeds. We introduce KQE-2, a training-free hybrid quantum-classical framework for reproducible whole-transcriptome clustering. KQE-2 maps cells into entanglement-free quantum states, enabling exact feature evaluation on classical hardware and direct checks on a quantum processor. Theoretically, we prove that removing entanglement is necessary and sufficient to bound single-qubit feature variance locally. Practically, while retraining scVI shifted 14% of cells and altered rare-type markers and drug targets, KQE-2 delivered identical biology across runs. On standard highly variable genes, the quantum encoding alone raised accuracy on a developing cortex from 0.61 to 0.79. KQE-2 scales to 11.4 million nuclei on one server, outperforming the compared methods on eight of ten complete atlases (and within the best method's run-to-run range on two), and leads on six even under standard downstream clustering.
AI agents store text as embedding vectors and compress them at scale. A compression is accepted when each item's nearest neighbors survive, but agents also consolidate, delete, and compare memories, tasks that depend on which items lie far apart. We evaluate both ends with two label-free fidelities from our prior work: the local fidelity $L$ at 10 neighbors and the global fidelity $G$ at 30 to 50 percent of the memory. At 96 bytes per passage, rescored binary codes reach an $L$ of 0.97 yet move 10.1 percent of passages to another theme; PCA with 8-bit codes, at an $L$ of 0.77, moves 1.7 percent. Rescoring leaves the stored codes, and thus $G$, unchanged. We prove that across the $G$ band, $1-ν_k$ is at most 2 to 2.18 times the square root of the near-far rank-violation rate, and that this rate follows the distance noise of the compression (correlation 0.979). Our locality-aware quantization (LAQ) turns the bound into a hinge objective on the codebooks of an OPQ index, keeping its bytes, rotation, and search. To our knowledge, LAQ is the first quantizer whose objective comes from a proven bound on the far end. Reconstruction alone raises $G$ in 0 of 52 held-out runs; the far hinge raises it in all 52. LAQ raises $G$ in all 52 ($p=8.5\times 10^{-4}$ over 13 memory-encoder groups), including the external FinDER memory, has the highest $G$ of seven equal-size quantizers in all 12 Multi-Doc-2025 runs, scales to a million passages, and keeps evidence recall.
Dimension reduction rests on a claim: t-SNE and UMAP preserve local structure, PCA global structure. Our DLP curve is the share of each point's k nearest neighbors a map keeps. Corrected for chance, it gives L at k=10 and G over 30 to 50% of the data, local and global fidelity. At the midpoint the curve is provably a rank correlation of distances. The LG reversal test decides, with a stated error rate, which of two maps is local and which global. On twelve datasets of up to 1.38 million points, G agrees with established global scores at 0.84 and 0.93, and the area under R_NX at 0.22 and 0.30. The entity fidelity E, read at each point's entity size, predicts which entities a map loses beyond L and G where entity sizes differ. In an agent memory of one million passages, t-SNE and PCA cross at 150,000 passages (p=2.6e-5).