The problem of cleaning impaired speech is crucial for various applications such as speech recognition, telecommunication, and assistive technologies. In this paper, we propose a novel approach that combines Pareto-optimized deep learning with non-negative matrix factorization (NMF) to effectively reduce noise in impaired speech signals while preserving the quality of the desired speech. Our method begins by calculating the spectrogram of a noisy voice clip and extracting frequency statistics. A threshold is then determined based on the desired noise sensitivity, and a noise-to-signal mask is computed. This mask is smoothed to avoid abrupt transitions in noise levels, and the modified spectrogram is obtained by applying the smoothed mask to the signal spectrogram. We then employ a Pareto-optimized NMF to decompose the modified spectrogram into basis functions and corresponding weights, which are used to reconstruct the clean speech spectrogram. The final noise-reduced waveform is obtained by inverting the clean speech spectrogram. Our proposed method achieves a balance between various objectives, such as noise suppression, speech quality preservation, and computational efficiency, by leveraging Pareto optimization in the deep learning model. The experimental results demonstrate the effectiveness of our approach in cleaning alaryngeal speech signals, making it a promising solution for various real-world applications.