A Quantum Generative Framework for Modeling Single-Cell Transcriptomes with Gene-Gene and Cell-Cell Interactions

Abstract: Single-cell RNA sequencing (scRNA-seq) data simulation is limited by classical methods that rely on linear correlations, failing to capture the intrinsic, nonlinear dependencies and the simultaneous gene-gene and cell-cell interactions. We introduce qSimCells, a novel hybrid quantum-classical simulator that leverages quantum entanglement to model single-cell transcriptomes. The core innovation is a quantum kernel that uses a parameterized quantum circuit with CNOT gates to encode complex, nonlinear gene regulatory network (GRN) and cell-cell communication topologies with explicit directionality (causality). The synthetic data exhibits non-classical dependencies that challenge standard analysis. We demonstrated that classical correlation methods (Pearson and Spearman) failed to reconstruct the complete programmed quantum causal paths, instead reporting spurious statistical artifacts driven by high base-gene expression probabilities. Applying CellChat2.0 to the simulated cell-cell communication validated the true mechanistic links by showing a robust, relative increase in communication probability (up to 75-fold) only when the quantum entanglement was active. This work confirms that the quantum kernel is essential for creating high-fidelity ground truth data, highlighting the need for advanced inference techniques to capture the complex, non-classical dependencies inherent in gene regulation.