Spinal diseases such as spinal degeneration and scoliosis might require pedicle screw placement (PSP) as a crucial step during surgical interventions, depending on the severity. This procedure requires the drilling of a hole for placing the screw. Thanks to imaging modalities such as computed tomography and intraoperative fluoroscopy, moving from an open approach to minimally invasive surgery (MIS) has been possible and has reduced patient complications after surgery. Still, it suffers from a lack of visual feedback for the surgeon, whereas robotic-assisted spine surgery combined with such imaging modalities can improve surgical outcomes for PSP. Yet, in such MIS procedures, physical motion, such as breathing motion, can induce shifts and deformations in the spine, leading to operation errors of approximately 2-3 mm [1]. In order to correctly identify the entry point, breathing motion needs to be compensated for. External sensors, such as an optical tracking system or range imaging, can be used to measure the motion of the skin or neighboring vertebrae, close to the entry point [2], [3]. However, Saghbiny et al. showed that the amplitude of breathing motion changes over vertebrae and has a variation of 68% from the lumbar to thoracic vertebrae [4]. Therefore, this work develops an approach for estimating the motion of each entry point, enhancing the accuracy. The proposed method uses a long short-term memory network (LSTM) on top of the inner control loop to estimate breathing motion parameters for each pedicle drilling individually, and its output is utilized to update the motion model for motion compensation during robot-assisted drilling for MIS-PSP.