Unaligned Sequence Similarity Search Using Deep Learning

• Main Authors: Senter, James K, Royalty, Taylor M, Steen, Andrew D, Sadovnik, Amir
• Format: Journal Article
• Language: English
• Published: 15-09-2019
• Subjects: Computer Science - Learning; Statistics - Machine Learning
• DOI: 10.48550/arxiv.1909.06929

Gene annotation has traditionally required direct comparison of DNA sequences
between an unknown gene and a database of known ones using string comparison
methods. However, these methods do not provide useful information when a gene
does not have a close match in the database. In addition, each comparison can
be costly when the database is large since it requires alignments and a series
of string comparisons. In this work we propose a novel approach: using
recurrent neural networks to embed DNA or amino-acid sequences in a
low-dimensional space in which distances correlate with functional similarity.
This embedding space overcomes both shortcomings of the method of aligning
sequences and comparing homology. First, it allows us to obtain information
about genes which do not have exact matches by measuring their similarity to
other ones in the database. If our database is labeled this can provide labels
for a query gene as is done in traditional methods. However, even if the
database is unlabeled it allows us to find clusters and infer some
characteristics of the gene population. In addition, each comparison is much
faster than traditional methods since the distance metric is reduced to the
Euclidean distance, and thus efficient approximate nearest neighbor algorithms
can be used to find the best match. We present results showing the advantage of
our algorithm. More specifically we show how our embedding can be useful for
both classification tasks when our labels are known, and clustering tasks where
our sequences belong to classes which have not been seen before.