High resolution cervical auscultation is a very promising noninvasive method for dysphagia screening and aspiration detection, as it does not involve the use of harmful ionizing radiation approaches. Automatic extraction of swallowing events in cervical auscultation is a key step for swallowing analysis to be clinically effective. Using time-varying spectral estimation of swallowing signals and deep feed forward neural networks, we propose an automatic segmentation algorithm for swallowing accelerometry and sounds that works directly on the raw swallowing signals in an online fashion. The algorithm was validated qualitatively and quantitatively using the swallowing data collected from 248 patients, yielding over 3000 swallows manually labeled by experienced speech language pathologists. With a detection accuracy that exceeded 95%, the algorithm has shown superior performance in comparison to the existing algorithms and demonstrated its generalizability when tested over 76 completely unseen swallows from a different population. The proposed method is not only of great importance to any subsequent swallowing signal analysis steps, but also provides an evidence that such signals can capture the physiological signature of the swallowing process.