Deep Learning Proteins using a Triplet-BERT network

Modern sequencing technology has produced a vast quantity of proteomic data, which has been key to the development of various deep learning models within the field. However, there are still challenges to overcome with regards to modelling the properties of a protein, especially when labelled resources are scarce. Developing interpretable deep learning models is an essential criterion, as proteomics research requires methods to understand the functional properties of proteins. The ability to derive quality information from both the model and the data will play a vital role in the advancement of proteomics research. In this paper, we seek to leverage a BERT model that has been pre-trained on a vast quantity of proteomic data, to model a collection of regression tasks using only a minimal amount of data. We adopt a triplet network structure to fine-tune the BERT model for each dataset and evaluate its performance on a set of downstream task predictions: plasma membrane localisation, thermostability, peak absorption wavelength, and enantioselectivity. Our results significantly improve upon the original BERT baseline as well as the previous state-of-the-art models for each task, demonstrating the benefits of using a triplet network for refining such a large pre-trained model on a limited dataset. As a form of white-box deep learning, we also visualise how the model attends to specific parts of the protein and how the model detects critical modifications that change its overall function.