Protein sequencing

Gene

Deep learning

Machine learning

Data mining

Artificial intelligence

Economics

Peptide sequence

Set (abstract data type)

Political science

Chemistry

Management

Programming language

Pure mathematics

Representation (politics)

Code (set theory)

Class (philosophy)

Sequence (biology)

Task (project management)

Mathematics

Computer science

Source code

Genetics

Biochemistry

Biology

Politics

Field (mathematics)

Bioinformatics

Motivation Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step. Results We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies. Availability and implementation Source code is available under https://github.com/nstrodt/UDSMProt. Supplementary information Supplementary data are available at Bioinformatics online.

UDSMProt: universal deep sequence models for protein classification