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The Hubble Space Telescope (HST) survey Measuring Young Stars in Space and Time (MYSST) entails some of the deepest photometric observations of extragalactic star formation, capturing even the lowest mass stars of the active star-forming complex N44 in the Large Magellanic Cloud. We employ the new MYSST stellar catalog to identify and characterize the content of young pre-main-sequence (PMS) stars across N44 and analyze the PMS clustering structure. To distinguish PMS stars from more evolved line of sight contaminants, a non-trivial task due to several effects that alter photometry, we utilize a machine learning classification approach. This consists of training a support vector machine (SVM) and a random forest (RF) on a carefully selected subset of the MYSST data and categorize all observed stars as PMS or non-PMS. Combining SVM and RF predictions to retrieve the most robust set of PMS sources, we find $\sim26,700$ candidates with a PMS probability above 95% across N44. Employing a clustering approach based on a nearest neighbor surface density estimate, we identify 18 prominent PMS structures at $1$ $σ$ significance above the mean density with sub-clusters persisting up to and beyond $3$ $σ$ significance. The most active star-forming center, located at the western edge of N44's bubble, is a subcluster with an effective radius of $\sim 5.6$ pc entailing more than 1,100 PMS candidates. Furthermore, we confirm that almost all identified clusters coincide with known H II regions and are close to or harbor massive young O stars or YSOs previously discovered by MUSE and Spitzer observations.