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Prediction of protein secondary structure from the amino acid sequence is a classical bioinformatics problem.
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Kabsch, W and Sander, C · 1983
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Predicting the secondary structure of globular proteins using neural network models
Qian, N and Sejnowski, T J · 1988
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Learning long-term dependencies with gradient descent is difficult
Bengio, Y, Simard, P, and Frasconi, P · 1994
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LONG SHORT-TERM MEMORY
Hochreiter, S, urgen Schmidhuber, J, and Elvezia, C · 1997
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Bidirectional recurrent neural networks
Schuster, M and Paliwal, KK · 1997
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Exploiting the past and the future in protein secondary structure prediction
Baldi, P, Brunak, S, and Frasconi, P · 1999
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Evaluation and improvement of multiple sequence methods for protein secondary structure prediction
Cuff, JA and Barton, GJ · 1999
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Protein secondary structure prediction based on position-specific scoring matrices
Jones, DT · 1999
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A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach
Hua, S and Sun, Z · 2001
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Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles
Pollastri, Gianluca, Przybylski, Darisz, Rost, Burkhard, and Baldi, Pierre · 2002
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Conditional random fields: Probabilistic models for segmenting and labeling sequence data
Lafferty, John, McCallum, Andrew, and Pereira, Fernando C N · 2006
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Conditional neural fields
Peng, J, Bo, L, and Xu, J · 2009
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Hidden-unit conditional random fields
Maaten, L, Welling, M, and Saul, LK · 2011
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Protein 8-class secondary structure prediction using conditional neural fields
Wang, Zhiyong, Zhao, Feng, Peng, Jian, and Xu, Jinbo · 2011
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Deep Generative Stochastic Networks Trainable by Backprop
Bengio, Yoshua and Thibodeau-Laufer, Éric · 2013
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Generating sequences with recurrent neural networks
Graves, Alex · 2013
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How to Construct Deep Recurrent Neural Networks
Pascanu, Razvan, Gulcehre, Caglar, Cho, Kyunghyun, and Bengio, Yoshua · 2013
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Towards end-to-end speech recognition with recurrent neural networks
Graves, A and Jaitly, N · 2014
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Sequence to sequence learning with neural networks
Sutskever, I, Vinyals, O, and Le, QVV · 2014
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Bastien, Frédéric, Lamblin, Pascal, Pascanu, Razvan, Bergstra, James, Goodfellow, Ian, Bergeron, Arnaud, Bouchard, Nicolas, Warde-Farley, David, and Bengio, Yoshua · 2012
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Supervised sequence labelling with recurrent neural networks
Graves, A · 2012
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ADADELTA: An Adaptive Learning Rate Method
Zeiler, Matthew D · 2012
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Deep Supervised and Convolutional Generative Stochastic Network for Protein Secondary Structure Prediction
Troyanskaya, Olga G · 2014
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Zaremba, Wojciech and Sutskever, Ilya · 2014
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