The article develops a comprehensive methodology for analyzing and forecasting technological development based on the evolutionary analysis of patent landscapes. A conceptual model of sustainable development of the innovative technologies market is proposed, based on the transformation of the entrepreneurial environment and synergistic interaction of actors of interdisciplinary scientific and technical programs. A system analysis of the semantic network of citing patents and publications within the framework of the target interdisciplinary program in the chemical engineering sphere was carried out, which revealed a stable increase in the demand for scientific results. To overcome the risks of information overload of actors of the national innovation system, methods of adaptive management of knowledge flows are proposed based on forecasting disturbances in the process of innovation diffusion. Mathematical models of the reliability of the national innovation system have been developed, including algorithms for decomposition into segments and analysis of series-parallel connections, which allows to significantly increase the efficiency of calculating the conditions of system operability in the context of global transformation. The key role of public-private partnership is substantiated and fiscal mechanisms for minimizing risks in integrating the results of intellectual activity into economic circulation are proposed.