Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Align-gram : Rethinking the Skip-gram Model for Protein Sequence
  Analysis   Background: The inception of next generations sequencing technologies have
exponentially increased the volume of biological sequence data. Protein
sequences, being quoted as the `language of life', has been analyzed for a
multitude of applications and inferences.
  Motivation: Owing to the rapid development of deep learning, in recent years
there have been a number of breakthroughs in the domain of Natural Language
Processing. Since these methods are capable of performing different tasks when
trained with a sufficient amount of data, off-the-shelf models are used to
perform various biological applications. In this study, we investigated the
applicability of the popular Skip-gram model for protein sequence analysis and
made an attempt to incorporate some biological insights into it.
  Results: We propose a novel $k$-mer embedding scheme, Align-gram, which is
capable of mapping the similar $k$-mers close to each other in a vector space.
Furthermore, we experiment with other sequence-based protein representations
and observe that the embeddings derived from Align-gram aids modeling and
training deep learning models better. Our experiments with a simple baseline
LSTM model and a much complex CNN model of DeepGoPlus shows the potential of
Align-gram in performing different types of deep learning applications for
protein sequence analysis.

33
The categories of this paper are: plasm-ph
8
The categories of this paper are: hep-ex
4
The categories of this paper are: cond-mat
34
The categories of this paper are: chem-ph
12
The categories of this paper are: nucl-th
17
The categories of this paper are: q-fin
14
The categories of this paper are: math-ph
19
The categories of this paper are: eess
32
The categories of this paper are: atom-ph
28
The categories of this paper are: alg-geom
25
The categories of this paper are: patt-sol
26
The categories of this paper are: bayes-an
5
The categories of this paper are: gr-qc
15
The categories of this paper are: nucl-ex
23
The categories of this paper are: solv-int
11
The categories of this paper are: hep-lat