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Inter-beat interval (IBI) measurement enables estimation of heart-tare variability (HRV) which, in turn, can provide early indication of potential cardiovascular diseases (CVDs). However, extracting IBIs from noisy signals is challenging since the morphology of the signal gets distorted in the presence of noise. Electrocardiogram (ECG) of a person in heavy motion is highly corrupted with noise, known as motion-artifact, and IBI extracted from it is inaccurate. As a part of remote health monitoring and wearable system development, denoising ECG signals and estimating IBIs correctly from them have become an emerging topic among signal-processing researchers. Apart from conventional methods, deep-learning techniques have been successfully used in signal denoising recently, and diagnosis process has become easier, leading to accuracy levels that were previously unachievable. We propose a deep-learning approach leveraging tiramisu autoencoder model to suppress motion-artifact noise and make the R-peaks of the ECG signal prominent even in the presence of high-intensity motion. After denoising, IBIs are estimated more accurately expediting diagnosis tasks. Results illustrate that our method enables IBI estimation from noisy ECG signals with SNR up to -30 dB with average root mean square error (RMSE) of 13 milliseconds for estimated IBIs. At this noise level, our error percentage remains below 8% and outperforms other state-of-the-art techniques.