1. A compound property prediction apparatus comprising: a memory storing a training sample library in which a parameter value relating to a chemical structure and a value of a prediction item are preregistered for each individual one of a plurality of training samples; an input device which takes data concerning an unknown sample as input; a processor, coupled to said memory and said input device, programmed to calculate a parameter value of said unknown sample, based on said input data; and, based on said parameter value, calculate a degree of similarity between said unknown sample and individual training samples; construct a sub-sample set by extracting training samples whose degree of similarity to said unknown sample is not smaller than a threshold that starts at a predetermined value and is reduced as necessary to ensure that a predetermined minimum number of the training samples are included in the sub-sample set; construct a prediction model by performing data analysis on said sub-sample set; and calculate a prediction value for said prediction item by applying the prediction model to said unknown sample.