Sample-based quantum diagonalization (SQD), an extension of quantum selected configuration interaction (QSCI), is a promising hybrid quantum-classical paradigm for molecular ground-state energies. By replacing variational optimization with quantum sampling, QSCI avoids barren plateaus and directly reconstructs correlated wavefunctions. However, existing configuration recovery mainly enforces symmetry constraints without targeting the most physically relevant configurations, often yielding oversized subspaces and costly classical diagonalization. We introduce QSCI-RBM, a compact subspace generation protocol based on Restricted Boltzmann Machines (RBMs), and integrate it within Density Matrix Embedding Theory (DMET). The RBM learns the distribution of dominant determinants from hardware samples, generating high-probability configurations. Sampling was performed on IBM Heron R1 (ibm_torino) for CH₅NO, R2 (ibm_fez) for C₂H₄, and R3 (ibm_boston) for the larger H₂O benchmark and the protein-ligand system. After validating on these benchmarks of increasing active-space size, we simulate the inhibitor Carmofur bound to the SARS-CoV-2 main protease (Mpro), fragmented into ten DMET impurities. Both DMET-QSCI-RBM and a DMET-SQD baseline reach chemical-potential self-consistency within four μ-iterations. At the converged chemical potential, DMET-QSCI-RBM lies within 0.05 mHa of DMET-FCI while accessing on average only 0.22% of the symmetry-preserving configuration space, versus 0.55 mHa at 33.0% for DMET-SQD, leading to a ∼153-fold subspace reduction. RBM-assisted expansion thus yields far more compact hardware-derived determinant spaces at equal or better accuracy, reducing classical overhead for scalable quantum embedding of biological systems on real hardware.