Amino acid encoding for deep learning applications

BMC Bioinformatics
Hesham ElAbdMareike Wendorff

Abstract

The number of applications of deep learning algorithms in bioinformatics is increasing as they usually achieve superior performance over classical approaches, especially, when bigger training datasets are available. In deep learning applications, discrete data, e.g. words or n-grams in language, or amino acids or nucleotides in bioinformatics, are generally represented as a continuous vector through an embedding matrix. Recently, learning this embedding matrix directly from the data as part of the continuous iteration of the model to optimize the target prediction - a process called 'end-to-end learning' - has led to state-of-the-art results in many fields. Although usage of embeddings is well described in the bioinformatics literature, the potential of end-to-end learning for single amino acids, as compared to more classical manually-curated encoding strategies, has not been systematically addressed. To this end, we compared classical encoding matrices, namely one-hot, VHSE8 and BLOSUM62, to end-to-end learning of amino acid embeddings for two different prediction tasks using three widely used architectures, namely recurrent neural networks (RNN), convolutional neural networks (CNN), and the hybrid CNN-RNN. By using different ...Continue Reading

References

Oct 4, 2005·Nature Reviews. Immunology·Walter ReithJean-Marc Waldburger
Mar 24, 2017·Nucleic Acids Research·Haoyang Zeng, David K Gifford
Jun 16, 2017·BMC Bioinformatics·Wen Torng, Russ B Altman
Jan 10, 2018·Immunology·Kamilla Kjaergaard JensenMorten Nielsen
Sep 25, 2018·Nature Biotechnology·Ryan PoplinMark A DePristo
Nov 6, 2018·Nucleic Acids Research·UNKNOWN UniProt Consortium
Nov 14, 2018·Bioinformatics·Somaye HashemifarJinbo Xu
Oct 23, 2019·Nature Methods·Ethan C AlleyGeorge M Church
May 29, 2019·BioRxiv : the Preprint Server for Biology·A. RivesRob Fergus

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Citations

Dec 29, 2020·Bioinformatics·Roman FeldbauerThomas Rattei
Sep 18, 2020·Proteomics·Bo WenBing Zhang
Apr 13, 2021·Computational and Structural Biotechnology Journal·Sangsoo LimSun Kim
Apr 15, 2021·Annual Review of Chemical and Biomolecular Engineering·Margarita PertsevaSai T Reddy

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Software Mentioned

blastp
Adam
TensorFlow
NetMHCIIpan
ProtVec
BLOSUM
word2vec
Keras

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