| The regional innovation system (RIS) is a vital component of the national innovation system, as well as the base of the development of the regional economy. At present, the shortage of human resources and financial resources is the main obstruction for the improvement of the innovative capacity of the RIS. Meanwhile, the structure of both inputs and outputs of Regional Innovation System (RIS) gradually becomes a vital factor influencing the improvement of Resources Allocation Efficiency (RAE). Due to certain constrains of macroeconomic factors, the shortage of the human resources and financial resources can not be met in a short period. Consequently, the strategy of the improvement of the RAE in RIS, analyzed by the view of the structure of the inputs and the outputs of the RIS, is a very heated topic, influencing both the innovative efforts of the firms and the sustainable development of the regional economy.At present, the research on the strategy of the resources allocation focuses on the evaluation of the RAE and the regional innovation performance of all provinces in China. The research using the cross-regional data cannot provide suitable policy suggestion, since the research ignores the regional features of production and technology, such as GDP, population and so on. Because most of the former research used the cross-regional data, did not give enough attention to the regional features, the conclusions of these researches lose some effectiveness to some extent. So, the paper, using the data from 1995 to 2005 of Shanghai regional innovation system and Jilin regional innovation system, analyzes the strategy of the resources allocation in the RIS, and improves the drawbacks of the former researches using the cross-regional data, and makes the policy suggestion more feasible in practice.Firstly, we make a dissertation review to relevant literature about the resources allocation and innovation mechanism of regional innovation system. Reviews about resource allocation efficiency and other vital influential factors are necessary for evaluating the contribution and shortage of former literature. Based on this review, we emphasize the importance of discipline and mechanism of resource allocation for the performance of regional innovation system.Secondly, the paper, using the Exploratory Factor Analysis (EFA), analyzes the structures of the inputs and outputs, and makes data reduction for the evaluation of the resources allocation. We recognize two factors of RIS inputs indictors, named as"Financial Resources Inputs Factor"and"Human Resources Inputs Factor", and three factors of RIS outputs indictors, named as"Science and Technological Outputs Quantity Factor"and"Science and Technological Outputs Quality Factor", and"industrial outputs factor".Thirdly, the paper, based on analyzing the structure of the inputs and outputs by the method of Exploratory Factor Analysis (EFA), evaluates the resources allocation efficiency of the regional innovation system from 1995 to 2004 by utilizing the Data Envelopment Analysis Benchmarking (DEA-Benchmarking) method. Based on the empirical results, the paper proposes three disciplines, as well as four propositions: firstly, the amount of the financial inputs should be determined according to the stock of the human resources; secondly, the policy-maker should consider which stage the RIS is in. Precisely, the enhancement of commercialization of S&T, the increase of S&T outputs and the improvement of quality of the S&T outputs of the regional innovation system should be, in order, the main focus to improve the RAE, according to the stage of the development of the RIS; thirdly, it is necessary to reduce the unreasonable input due to the rapid development of the economy, in order to decrease the rent-seek behavior of talent; fourthly, the policy maker should pay more attention to the coupling mechanism of the basic research and innovation behaviors, for the sustainable development of the regional innovation system.Fourthly, the paper constructs the equation model of the input factors and the output factors, and analyzes the innovation mechanism of the regional innovation system. Compared the original model with the modified model, the paper conclude four disciplines: firstly, the relationship between the resources input and the output of the regional innovation system is not linear, and should be considered in the systematic framework; secondly, the human resources input of the regional innovation system moderates the relationship between the financial resources input of the regional innovation system and the quality of the S&T outputs of the regional innovation system. The more the human resources input of the regional innovation system is, the more significant the influence of the financial resources input of the regional innovation system to the quality of the S&T outputs of the regional innovation system; thirdly, the financial resources input of the regional innovation system moderates the relationship between the human resources input of the regional innovation system and the commercialization of S&T of the regional innovation system. The more the financial resources input of the regional innovation system is, the more significant the influence of the human resources input of the regional innovation system to the commercialization of S&T of the regional innovation system; fourthly, the degree of the match of the human resources input and financial resources input have significant influence on the resources allocation efficiency of the regional innovation system.Finally, the paper, using the discrimination analysis method, constructs the model of development stage discrimination model, taking the Jilin regional innovation system as instance, in order to analyze the stage characteristics and the evolution process of regional innovation system. Based on this research, the paper gives a contingent policy advice for local regional innovation system development.
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