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Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications.
The Viterbi algorithm
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Handwritten digit recognition with a back-propagation network
Yan LeCun, Bernhard Boser, John Denker, R. Howard, Wayne Habbard, Lawrence Jackel, and Donnie Henderson · 1990
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Backpropagation through time: what it does and how to do it
Paul Werbos · 1990
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Long short-term memory
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Mike Schuster and Kuldip Paliwal · 1997
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A Maximum Entropy Approach to Named Entity Recognition
Andrew Borthwick · 1999
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Named entity recognition through classifier combination
Radu Florian, Abe Ittycheriah, Hongyan Jing, and Tong Zhang · 2003
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Exploring deep knowledge resources in biomedical name recognition
Zhou GuoDong and Su Jian · 2004
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Introduction to the bio-entity recognition task at JNLPBA
Jin-Dong Kim, Tomoko Ohta, Yoshimasa Tsuruoka, Yuka Tateisi, and Nigel Collier · 2004
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Biomedical named entity recognition using conditional random fields and rich feature sets
Burr Settles · 2004
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Geoffrey Hinton and Ruslan Salakhutdinov · 2006
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Biocreative II gene mention tagging system at IBM Watson
Rie Ando · 2007
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BANNER: An executable survey of advances in biomedical named entity recognition
Robert Leaman and Graciela Gonzalez · 2008
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Why does unsupervised pre-training help deep learning?
Dumitru Erhan, Yoshua Bengio, Aaron Courville, Pierre-Antoine Manzagol, Pascal Vincent, and Samy Bengio · 2010
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Understanding the difficulty of training deep feedforward neural networks
Xavier Glorot and Yoshua Bengio · 2010
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Disambiguation in the biomedical domain: The role of ambiguity type
Mark Stevenson and Yikun Guo · 2010
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Natural language processing (almost) from scratch
Ronan Collobert, Jason Weston, Léon Bottou, Michael Karlen, Koray Kavukcuoglu, and Pavel Kuksa · 2011
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An improved corpus of disease mentions in PubMed citations
Rezarta Doğan and Zhiyong Lu · 2012
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ImageNet classification with deep convolutional neural networks
Alex Krizhevsky, Ilya Sutskever, and Geoffrey Hinton · 2012
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Gimli: open source and high-performance biomedical name recognition
David Campos, Sérgio Matos, and José Oliveira · 2013
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Generating sequences with recurrent neural networks
Alex Graves · 2013
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Distributed representations of words and phrases and their compositionality
TaggerOne: joint named entity recognition and normalization with semi-Markov models
Robert Leaman and Zhiyong Lu · 2016
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BioCreative V CDR task corpus: a resource for chemical disease relation extraction
Jiao Li, Yueping Sun, Robin J Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J Mattingly, Thomas C Wiegers, and Zhiyong Lu · 2016
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End-to-end sequence labeling via bi-directional LSTM-CNNs-CRF
Xuezhe Ma and Eduard Hovy · 2016
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Named entity recognition for novel types by transfer learning
Lizhen Qu, Gabriela Ferraro, Liyuan Zhou, Weiwei Hou, and Timothy Baldwin · 2016
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Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks
Qikang Wei, Tao Chen, Ruifeng Xu, Yulan He, and Lin Gui · 2016
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Adam: A method for stochastic optimization
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Semi-supervised sequence learning
Andrew Dai and Quoc Le · 2015
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Bidirectional LSTM-CRF models for sequence tagging
Zhiheng Huang, Wei Xu, and Kai Yu · 2015
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A neural network multi-task learning approach to biomedical named entity recognition
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Deep learning with word embeddings improves biomedical named entity recognition
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Transfer learning for biomedical named entity recognition with neural networks
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