PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
This work addresses a critical gap for researchers in computational biology and bioinformatics by providing a unified benchmark to accelerate progress in protein sequence analysis, though it is incremental as it builds on existing methods and datasets.
The authors tackled the lack of a standard benchmark for evaluating deep learning methods in protein sequence understanding by proposing PEER, a comprehensive multi-task benchmark, and found that large-scale pre-trained protein language models achieved the best performance for most tasks, with joint multi-task training further boosting results.
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark