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Also, ecosystem mapping studies involve either whole-network analysis at the macro-level or ego-network analysis at the micro-level, while few studies have investigated network community analysis at the meso-level. Therefore, this paper proposes a framework of Multi-layered Innovation Ecosystem Mapping (MIEM) to explore both knowledge and business ecosystems, thereby extending the analysis to the network communities. Based on multi-source heterogeneous data and machine learning, MIEM includes four steps in conducting the analysis: define the research scope and collect data; construct whole networks; identify communities; and recognize strategic roles. In particular, Newman topological clustering is adopted to identify network communities, and a strategic-role matrix is used to analyze the roles in a community. 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