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The superior spectral efficiency (SE) and user fairness feature of non-orthogonal multiple access (NOMA) systems are achieved by exploiting user clustering (UC) more efficiently. However, a random UC certainly results in a suboptimal solution while an exhaustive search method comes at the cost of high complexity, especially for systems of medium-to-large size. To address this problem, we develop two efficient unsupervised machine learning (ML) based UC algorithms, namely k-means++ and improved k-means++, to effectively cluster users into disjoint clusters in cell-free massive multiple-input multiple-output (CFmMIMO) system. Using full-pilot zero-forcing at access points, we derive the sum SE in closed-form expression taking into account the impact of intra-cluster pilot contamination, inter-cluster interference, and imperfect successive interference cancellation. To comprehensively assess the system performance, we formulate the sum SE optimization problem, and then develop a simple yet efficient iterative algorithm for its solution. In addition, the performance of collocated massive MIMO-NOMA (COmMIMO-NOMA) system is also characterized. Numerical results are provided to show the superior performance of the proposed UC algorithms compared to other baseline schemes. The effectiveness of applying NOMA in CFmMIMO and COmMIMO systems is also validated.