  Composed of amino acid chains that influence how they fold and thus dictating
their function and features, proteins are a class of macromolecules that play a
central role in major biological processes and are required for the structure,
function, and regulation of the body's tissues. Understanding protein functions
is vital to the development of therapeutics and precision medicine, and hence
the ability to classify proteins and their functions based on measurable
features is crucial; indeed, the automatic inference of a protein's properties
from its sequence of amino acids, known as its primary structure, remains an
important open problem within the field of bioinformatics, especially given the
recent advancements in sequencing technologies and the extensive number of
known but uncategorized proteins with unknown properties. In this work, we
demonstrate and compare the performance of several deep learning frameworks,
including novel bi-directional LSTM and convolutional models, on widely
available sequencing data from the Protein Data Bank (PDB) of the Research
Collaboratory for Structural Bioinformatics (RCSB), as well as benchmark this
performance against classical machine learning approaches, including k-nearest
neighbors and multinomial regression classifiers, trained on experimental data.
Our results show that our deep learning models deliver superior performance to
classical machine learning methods, with the convolutional architecture
providing the most impressive inference performance.
