Deep learning in bioinformatics

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Computer vision for high content screening

(2016) Oren Z. Kraus et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Guest Editorial Deep Learning in Medical Imaging: Overview and Future Promise of an Exciting New Technique

(2016) Hayit Greenspan et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

A Cross-Modality Learning Approach for Vessel Segmentation in Retinal Images

(2016) Qiaoliang Li et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Stacked Sparse Autoencoder (SSAE) for Nuclei Detection on Breast Cancer Histopathology Images

(2016) Jun Xu et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

(2016) Michael K. K. Leung et al.   PROCEEDINGS OF THE IEEE

Predicting protein functions using incomplete hierarchical labels

(2015) Guoxian Yu et al.   BMC BIOINFORMATICS

Describing Multimedia Content Using Attention-Based Encoder-Decoder Networks

(2015) Kyunghyun Cho et al.   IEEE TRANSACTIONS ON MULTIMEDIA

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Deep learning

(2015) Yann LeCun et al.   NATURE

Deep learning for regulatory genomics

(2015) Yongjin Park et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

Improving prediction of secondary structure, local backbone angles and solvent accessible surface area of proteins by iterative deep learning

(2015) Rhys Heffernan et al.   Scientific Reports

Predicting Response to Neoadjuvant Chemotherapy with PET Imaging Using Convolutional Neural Networks

(2015) Petros-Pavlos Ypsilantis et al.   PLoS One

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network

(2014) James Lyons et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

EEG-Based Emotion Recognition Using Deep Learning Network with Principal Component Based Covariate Shift Adaptation

(2014) Suwicha Jirayucharoensak et al.   TheScientificWorldJOURNAL

Deep learning for neuroimaging: a validation study

(2014) Sergey M. Plis et al.   Frontiers in Neuroscience

An insight into classification with imbalanced data: Empirical results and current trends on using data intrinsic characteristics

(2013) Victoria López et al.   INFORMATION SCIENCES

Connectomic reconstruction of the inner plexiform layer in the mouse retina

(2013) Moritz Helmstaedter et al.   NATURE

Deep architectures for protein contact map prediction

(2012) Pietro Di Lena et al.   BIOINFORMATICS

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

Learning Hierarchical Features for Scene Labeling

(2012) Clement Farabet et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Biomedical data privacy: problems, perspectives, and recent advances

(2012) B. A. Malin et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

The origin of extracellular fields and currents — EEG, ECoG, LFP and spikes

(2012) György Buzsáki et al.   NATURE REVIEWS NEUROSCIENCE

Modeling electroencephalography waveforms with semi-supervised deep belief nets: fast classification and anomaly measurement

(2011) D F Wulsin et al.   Journal of Neural Engineering

Convolutional Neural Networks for P300 Detection with Application to Brain-Computer Interfaces

(2010) H Cecotti et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Ensemble Learning with Active Example Selection for Imbalanced Biomedical Data Classification

(2010) Sangyoon Oh et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Neural Decoding with Hierarchical Generative Models

(2010) Marcel A. J. van Gerven et al.   NEURAL COMPUTATION

Classification of patterns of EEG synchronization for seizure prediction

(2009) Piotr Mirowski et al.   CLINICAL NEUROPHYSIOLOGY

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Learning long-range vision for autonomous off-road driving

(2009) Raia Hadsell et al.   Journal of Field Robotics

Exploratory Undersampling for Class-Imbalance Learning

(2008) Xu-Ying Liu et al.   IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART B-CYBERNETICS