In existing matrix factorization (MF)-based recommender systems, the user-item interaction matrix is factorized linearly into two low-ranked feature matrices to generate predictions or provide the users with personalized rankings of items. However, when MF methods are directly applied to sparse rating matrices, they cannot cope with the inherent structure of real-world user and item latent features. The efficiency of MF-based systems crucially depends on their capability to address sparsity issues. To this end, we propose, in this paper, a novel preference-based data imputation approach for effective MF-based Top-K recommendation. We apply MF on an imputed and denser rating matrix with only interesting items to users. We obtain these items by inferring the prior preferences of users, considering some biases that may impact their choices for items they interact with, and leveraging a powerful latent and non-linear feature extraction using a deep generative model. Experimental results on two real-world sparse datasets reveal that the proposed model significantly enhances the performance of Top-K recommendations and outperforms baselines with an average improvement margin of 6.45% and 3.91% in hit rate (HR) and normalized discounted cumulative gain (NDCG) evaluation metrics, respectively, averaging on all employed datasets.