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Machine learning is widely used to analyze biological sequence data.
Handwritten digit recognition with a back-propagation network
Cunn, Yann Le, Boser, B, Denker, JS, Henderson, D, Howard, RE, W, Hubbard., and Jackel, LD · 1990
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Amino acid substitution matrices from protein blocks
Henikoff, S and Henikoff, J G · 1992
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LONG SHORT-TERM MEMORY
Hochreiter, S, Schmidhuber, J, and Elvezia, C · 1997
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Bidirectional recurrent neural networks
Schuster, M and Paliwal, KK · 1997
Earlier work this paper cites.
Structure-derived substitution matrices for alignment of distantly related sequences
Prlić, A, Domingues, F S, and Sippl, M J · 2000
Earlier work this paper cites.
MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition
Höglund, Annette, Dönnes, Pierre, Blum, Torsten, Adolph, Hans-Werner, and Kohlbacher, Oliver · 2006
Earlier work this paper cites.
Locating proteins in the cell using TargetP, SignalP and related tools
Emanuelsson, Olof, Brunak, Sø ren, von Heijne, Gunnar, and Nielsen, Henrik · 2007
Earlier work this paper cites.
Visualizing high-dimensional data using t-sne
Van Der Maaten, L J P and Hinton, G E · 2008
Earlier work this paper cites.
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
Blum, Torsten, Briesemeister, Sebastian, and Kohlbacher, Oliver · 2009
Earlier work this paper cites.
SherLoc2: a high-accuracy hybrid method for predicting subcellular localization of proteins
Briesemeister, Sebastian, Blum, Torsten, Brady, Scott, Lam, Yin, Kohlbacher, Oliver, and Shatkay, Hagit · 2009
Cited alongside, same era.
Rectified linear units improve restricted boltzmann machines
Nair, Vinod and Hinton, Geoffrey E · 2010
Cited alongside, same era.
Uniprot knowledgebase: a hub of integrated protein data
Magrane, Michele, UniProt Consortium, et al · 2011
Cited alongside, same era.
SignalP 4.0: discriminating signal peptides from transmembrane regions
Petersen, TN, Brunak, Søren, von Heijne, Gunnar, and Nielsen, H · 2011
Cited alongside, same era.
Theano: new features and speed improvements
Bastien, Frédéric, Lamblin, Pascal, Pascanu, Razvan, Bergstra, James, Goodfellow, Ian, Bergeron, Arnaud, Bouchard, Nicolas, Warde-Farley, David, and Bengio, Yoshua · 2012
Cited alongside, same era.
Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion
Thomsen, M. C. F and Nielsen, M · 2012
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Generating sequences with recurrent neural networks
Graves, Alex · 2013
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Neural Machine Translation by Jointly Learning to Align and Translate
Bahdanau, Dzmitry, Cho, Kyunghyun, and Bengio, Yoshua · 2014
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Towards end-to-end speech recognition with recurrent neural networks
Graves, A and Jaitly, N · 2014
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Context-dependent pre-trained deep neural networks for large-vocabulary speech recognition
Dahl, GE, Yu, D, Deng, L, and Acero, A · 2012
Cited alongside, same era.
LocTree2 predicts localization for all domains of life
Goldberg, Tatyana, Hamp, Tobias, and Rost, Burkhard · 2012
Cited alongside, same era.
Supervised sequence labelling with recurrent neural networks
Graves, A · 2012
Cited alongside, same era.
Imagenet classification with deep convolutional neural networks
Krizhevsky, A, Sutskever, I, and Hinton, GE · 2012
Cited alongside, same era.
Recurrent neural network regularization
Zaremba, W, Sutskever, I, and Vinyals, O
Cited in the paper.
Learning to Discover Efficient Mathematical Identities
Zaremba, Wojciech, Kurach, Karol, and Fergus, Rob
Cited in the paper.
Kingma, Diederik and Ba, Jimmy · 2014
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Sequence to sequence learning with neural networks
Sutskever, I, Vinyals, O, and Le, QVV · 2014
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The human splicing code reveals new insights into the genetic determinants of disease
Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K. C., Hua, Y., Gueroussov, S., Najafabadi, H. S., Hughes, T. R., Morris, Q., Barash, Y., Krainer, A. R., Jojic, N., Scherer, S. W., Blencowe, B. J., and Frey, B. J · 2014
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Zaremba, Wojciech and Sutskever, Ilya · 2014
Later among the works it cites.