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The geospace environment is volatile and highly driven. Space weather has effects on Earth's magnetosphere that cause a dynamic and enigmatic response in the thermosphere, particularly on the evolution of neutral mass density. Many models exist that use space weather drivers to produce a density response, but these models are typically computationally expensive or inaccurate for certain space weather conditions. In response, this work aims to employ a probabilistic machine learning (ML) method to create an efficient surrogate for the Thermosphere Ionosphere Electrodynamics General Circulation Model (TIE-GCM), a physics-based thermosphere model. Our method leverages principal component analysis to reduce the dimensionality of TIE-GCM and recurrent neural networks to model the dynamic behavior of the thermosphere much quicker than the numerical model. The newly developed reduced order probabilistic emulator (ROPE) uses Long-Short Term Memory neural networks to perform time-series forecasting in the reduced state and provide distributions for future density. We show that across the available data, TIE-GCM ROPE has similar error to previous linear approaches while improving storm-time modeling. We also conduct a satellite propagation study for the significant November 2003 storm which shows that TIE-GCM ROPE can capture the position resulting from TIE-GCM density with < 5 km bias. Simultaneously, linear approaches provide point estimates that can result in biases of 7 - 18 km.