On the basis of the scientific and technologic statistical data of Fujian province from 2001 to 2008, the present situation of scientific and technological funding input was comprehensively analyzed, then the optimization and configuration of scientific and technological funding input was studied by Analytic Hierarchy Process and Grey System Theory. The result shows that the grey relevancy of funding input and output was the maximum for research institute in different activity subjects, and was the maximum for fundamental research in different activity types. So we should optimize the funding input configuration in these two aspects to get the larger output.
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