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This paper shows how one can directly apply natural language processing (NLP) methods to classification problems in cheminformatics.
Electrotopological state indices for atom types: A novel combination of electronic, topological, and valence state information
Lowell Hall and Lemont Kier · 1995
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The chemistry development kit (cdk): An open-source java library for chemo- and bioinformatics
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Novel 2d fingerprints for ligand-based virtual screening
Todd Ewing, J. Christian Baber, and Miklos Feher · 2006
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Chemical substructures that enrich for biological activity
Justin Klekota and Frederick Roth · 2008
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Smiles-based optimal descriptors: Qsar modeling of carcinogenicity by balance of correlations with ideal slopes
Andrey Toropov, Alla Toropova, and E Benfenati · 2010
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Strategies for training large scale neural network language models
Tomas Mikolov, Anoop Deoras, Daniel Povey, Lukás Burget, and Jan Cernocký · 2011
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Rnnlm-recurrent neural network language modeling toolkit
Tomas Mikolov, Stefan Kombrink, Anoop Deoras, Lukar Burget, and Jan Cernocky · 2011
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Unsupervised feature learning and deep learning: A review and new perspectives
Yoshua Bengio, Aaron Courville, and Pascal Vincent · 2012
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Robust optimization of svm hyperparameters in the classification of bioactive compounds
Wojciech Marian Czarnecki, Sabina Podlewska, and Andrzej Bojarski · 2015
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Semi-supervised sequence learning
Andrew Dai and Quoc Viet Le · 2015
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Convolutional networks on graphs for learning molecular fingerprints
David Kristjanson Duvenaud, Dougal Maclaurin, Jorge Aguilera-Iparraguirre, Rafael Gómez-Bombarelli, Timothy Hirzel, Alán Aspuru-Guzik, and Ryan Prescott Adams · 2015
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Deep convolutional networks on graph-structured data
Mikael Henaff, Joan Bruna, and Yann LeCun · 2015
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Effective use of word order for text categorization with convolutional neural networks
Rie Johnson and Tong Zhang · 2015
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Grégoire Mesnil, Tomas Mikolov, Marc’Aurelio Ranzato, and Yoshua Bengio · 2014
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Thomas Unterthiner, Andreas Mayr, Günter Klambauer, Marvin Steijaert, Jörg Wenger, Hugo Ceulemans, and Sepp Hochreiter · 2014
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Large-scale qsar study of aromatase inhibitors using smiles-based descriptors
Apilak Worachartcheewan, Prasit Mandi, Virapong Prachayasittikul, Alla Toropova, Andrey Toropov, and Chanin Nantasenamat · 2014
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Character-aware neural language models
Yoon Kim, Yacine Jernite, David Sontag, and Alexander Rush · 2015
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Exploring the limits of language modeling
Rafal Jozefowicz, Oriol Vinyals, Mike Schuster, Noam Shazeer, and Yonghui Wu · 2016
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