We present a new open-source, machine learning (ML) enhanced computational method for experimentalists to quickly analyze high-throughput small-angle scattering results from multicomponent nanoparticle mixtures and solutions at varying compositions and concentrations to obtain reconstructed 3D structures of the sample. This new method is an improvement over our original computational reverse-engineering analysis for scattering experiments (CREASE) method (ACS Materials Au2021, 1 (2 (2), ), 140−156), which takes as input the experimental scattering profiles and outputs a 3D visualization and structural characterization (e.g., real space pair-correlation functions, domain sizes, and extent of mixing in binary nanoparticle mixtures) of the nanoparticle mixtures. The new gene-based CREASE method reduces the computational running time by >95% as compared to the original CREASE and performs better in scenarios where the original CREASE method performed poorly. Furthermore, the ML model linking features of nanoparticle solutions (e.g., concentration, nanoparticles’ tendency to aggregate) to a computed scattering profile is generic enough to analyze scattering profiles for nanoparticle solutions at conditions (nanoparticle chemistry and size) beyond those that were used for the ML training. Finally, we demonstrate application of this new gene-based CREASE method for analysis of small-angle X-ray scattering results from a nanoparticle solution with unknown nanoparticle aggregation and small-angle neutron scattering results from a binary nanoparticle assembly with unknown mixing/segregation among the nanoparticles.