I'm an undergraduate biology student and my thesis is on designing a deep learning architecture to predict whether two proteins interact or not given their primary sequences. I have read some papers with different approaches to the problem including the paper [https://academic.oup.com/bioinformatics/article/35/14/i305/5529260] uses PIPR model which is the state of the art model for this problem in 2019 and recently in 2021 the paper [https://www.biorxiv.org/content/10.1101/2021.01.22.427866v1] uses D-SCRIPT which surpass PIPR with the aspect of the small dataset and has better generalization feature for many model organisms.
For my problem, I have two questions
- can you suggest to me the approach to build a model for my thesis. Should I follow these papers to build a model, how my model will be different from the models in the papers?
- Which architecture or model recently that the literature considers the most proper for the protein-protein interaction prediction approach?
I very much appreciate any help from everyone!