A method processes a signal represented as a graph by first determining a graph spectral transform based on the graph. In a spectral domain, parameters of a graph filter are estimated using a training data set of unenhanced and corresponding enhanced signals. The graph filter is derived based on the graph spectral transform and the estimated graph filter parameters. Then, the signal is processed using the graph filter to produce an output signal. The processing can enhance signals such as images by denoising or interpolating missing samples.