One embodiment of the present invention provides a system that predicts a manufacturing yield of a chip. During operation, the system first receives a chip layout. Next, the system identifies hotspots within the chip layout, wherein a hotspot is a location within the chip layout wherein a yield-indicative variable value falls in a low manufacturable range. The system then obtains yield scores for the hotspots, wherein a yield score indicates a failure probability for a corresponding hotspot. Next, the system predicts the manufacturing yield for the chip based on the hotspots and the yield scores for the hotspots.