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Intent-based networks that integrate sophisticated machine reasoning technologies will be a cornerstone of future wireless 6G systems. Intent-based communication requires the network to consider the semantics (meanings) and effectiveness (at end-user) of the data transmission. This is essential if 6G systems are to communicate reliably with fewer bits while simultaneously providing connectivity to heterogeneous users. In this paper, contrary to state of the art, which lacks explainability of data, the framework of neuro-symbolic artificial intelligence (NeSy AI) is proposed as a pillar for learning causal structure behind the observed data. In particular, the emerging concept of generative flow networks (GFlowNet) is leveraged for the first time in a wireless system to learn the probabilistic structure which generates the data. Further, a novel optimization problem for learning the optimal encoding and decoding functions is rigorously formulated with the intent of achieving higher semantic reliability. Novel analytical formulations are developed to define key metrics for semantic message transmission, including semantic distortion, semantic similarity, and semantic reliability. These semantic measure functions rely on the proposed definition of semantic content of the knowledge base and this information measure is reflective of the nodes' reasoning capabilities. Simulation results validate the ability to communicate efficiently (with less bits but same semantics) and significantly better compared to a conventional system which does not exploit the reasoning capabilities.