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As one of the most serious types of cyber attack, Advanced Persistent Threats (APT) have caused major concerns on a global scale. APT refers to a persistent, multi-stage attack with the intention to compromise the system and gain information from the targeted system, which has the potential to cause significant damage and substantial financial loss. The accurate detection and prediction of APT is an ongoing challenge. This work proposes a novel machine learning-based system entitled MLAPT, which can accurately and rapidly detect and predict APT attacks in a systematic way. The MLAPT runs through three main phases: (1) Threat detection, in which eight methods have been developed to detect different techniques used during the various APT steps. The implementation and validation of these methods with real traffic is a significant contribution to the current body of research; (2) Alert correlation, in which a …