The issue of missing data poses a great challenge on boosting performance and application of deep learning models in the {\em Knowledge Tracing} (KT) problem. However, there has been the lack of understanding on the issue in the literature. %are not sufficient studies tackling this problem. In this work, to address this challenge, we adopt a subject-based training method to split and impute data by student IDs instead of row number splitting which we call non-subject based training. The benefit of subject-based training can retain the complete sequence for each student and hence achieve efficient training. Further, we leverage two existing deep generative frameworks, namely variational Autoencoders (VAE) and Longitudinal Variational Autoencoders (LVAE) frameworks and build LSTM kernels into them to form LSTM-VAE and LSTM LVAE (noted as VAE and LVAE for simplicity) models to generate quality data. In LVAE, a Gaussian Process (GP) model is trained to disentangle the correlation between the subject (i.e., student) descriptor information (e.g., age, gender) and the latent space. The paper finally compare the model performance between training the original data and training the data imputed with generated data from non-subject based model VAE-NS and subject-based training models (i.e., VAE and LVAE). We demonstrate that the generated data from LSTM-VAE and LSTM-LVAE can boost the original model performance by about 50%. Moreover, the original model just needs 10% more student data to surpass the original performance if the prediction model is small and 50\% more data if the prediction model is large with our proposed frameworks.