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In this paper, a set of machine learning (ML) tools is applied to estimate the water saturation of shallow unconsolidated sediments at the Bátaapáti site in Hungary. Water saturation is directly calculated from the first factor extracted from a set of direct push logs by factor analysis. The dataset observed by engineering geophysical sounding tools as special variants of direct-push probes contains data from a total of 12 shallow penetration holes. Both one- and two-dimensional applications of the suggested method are presented. To improve the performance of factor analysis, particle swarm optimization (PSO) is applied to give a globally optimized estimate for the factor scores. Furthermore, by a hyperparameter estimation approach, some control parameters of the utilized PSO algorithm are automatically estimated by simulated annealing (SA) to ensure the convergence of the procedure. The result of the suggested ML-based log analysis method is compared and verified by an independent inversion estimate. The study shows that the PSO-based factor analysis aided by hyperparameter estimation provides reliable in situ estimates of water saturation, which may improve the solution of environmental end engineering problems in shallow unconsolidated heterogeneous formations. [ABSTRACT FROM AUTHOR]