Polishing apparatus using machine learning and compensation for pad thickness

Data received from an in-situ monitoring system includes, for each scan of a sensor, a plurality of measured signal values for a plurality of different locations on a layer. A thickness of a polishing pad is determined based on the data from the in-situ monitoring system. For each scan, a portion of the measured signal values are adjusted based on the thickness of the polishing pad. For each scan of the plurality of scans and each location of the plurality of different locations, a value is generated representing a thickness of the layer at the location. This includes processing the adjusted signal values using one or more processors configured by machine learning. A polishing endpoint is detected or a polishing parameter is modified based on the values representing the thicknesses at the plurality of different locations.