A method of polishing a substrate includes polishing a conductive layer on the substrate at a polishing station, monitoring the layer with an in-situ eddy current monitoring system to generate a plurality of measured signals values for a plurality of different locations on the layer, generating thickness measurements the locations, and detecting a polishing endpoint or modifying a polishing parameter based on the thickness measurements. The conductive layer is formed of a first material having a first conductivity. Generating includes calculating initial thickness values based on the plurality of measured signals values and processing the initial thickness values through a neural network that was trained using training data acquired by measuring calibration substrates having a conductive layer formed of a second material having a second conductivity that is lower than the first conductivity to generated adjusted thickness values.