In communications, innovative paradigm shifts have emerged in integrating various devices into the network to provide advanced and intelligent services. However, various security threats may occur that may not always be detected using traditional cryptographic techniques. Secure authentication is of paramount importance in modern wireless systems. This paper focusses on robust authentication in a timevarying communication environment where conventional authentication mechanisms are severely limited. We propose an Adaptive Neural Network (ANN) as an intelligent authentication process to improve detection accuracy. Specifically, a Data-Adaptive Matrix (DAM) is designed to track time-varying channel features. By utilizing a convolutional neural network as an intelligent authenticator, the proposed approach integrates deep feature extraction and attack detection, hence, leading to effective physical layer security. To evaluate the system, the ANN is prototyped on a universal software radio peripheral (USRP) and its authentication performance is evaluated in a conference room environment. Experimental results show that the ANN is effective in tackling the challenges of physical layer authentication under interference conditions, and is effective in time-varying environments. INDEX TERMS Convolutional neural network, physical layer security, intrusion detection, machine learning.