QuantumXCT: Learning Interaction-Induced State Transformation in Cell-Cell Communication via Quantum Entanglement and Generative Modeling

Abstract

Inferring cell-cell communication (CCC) from single-cell transcriptomics remains fundamentally limited by reliance on curated ligand-receptor databases, which primarily capture co-expression rather than the system-level effects of signaling on cellular states. Here, we introduce QuantumXCT, a hybrid quantum-classical generative framework that reframes CCC as a problem of learning interaction-induced state transformations between cellular state distributions. By encoding transcriptomic profiles into a high-dimensional Hilbert space, QuantumXCT trains parameterized quantum circuits to learn a unitary transformation that maps a baseline non-interacting cellular state to an interacting state. This approach enables the discovery of communication-driven changes in cellular state distributions without requiring prior biological assumptions. We validate QuantumXCT using both synthetic data with known ground-truth interactions and single-cell RNA-seq data from ovarian cancer-fibroblast co-culture model. The QuantumXCT model accurately recovered complex regulatory dependencies, including feedback structures, and identified dominant communication hubs such as the PDGFB-PDGFRB-STAT3 axis. Importantly, the learned quantum circuit is interpretable: its entangling topology was translated into biologically meaningful interaction networks, while post hoc contribution analysis quantified the relative influence of individual interactions on the observed state transitions. Notably, by shifting CCC inference from static interaction lookup to learning data-driven state transformations, QuantumXCT provides a generative framework for modeling intercellular communication. This work establishes a new paradigm for de novo discovery of communication programs in complex biological systems and highlights the potential of quantum machine learning in the context of single-cell biology.