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Table 4 Different encodings from deep learning models (see Table 1 for details)

From: Encodings and models for antimicrobial peptide classification for multi-resistant pathogens

Encoding

Description

Summary

Used in

Used along with

ProtVec

amino acid sequences are encoded as a distributed representation of k-mers

Density: +

Information: +

[124]

 

Voxel

structures of proteins are encoded as voxels

Density: o

Information: +

[125, 126]

 

Matrix

mimicks images by regarding the respective entries of PSSMs as pixel densities

Density: o

Information: +

[127, 129, 130]

PSSM

Autoencoder

extracts representative characteristics in order to reproduce the input as good as possible

Density: +

Information: o

[131]