A method of polishing a layer on the substrate at a polishing station includes the actions of monitoring the layer during polishing at the polishing station with an in-situ monitoring system to generate a plurality of measured signals for a plurality of different locations on the layer; generating, for each location of the plurality of different locations, an estimated measure of thickness of the location, the generating including processing the plurality of measured signals through a neural network; and at least one of detecting a polishing endpoint or modifying a polishing parameter based on each estimated measure of thickness.