Brendan J. Frey

According to our database1, Brendan J. Frey authored at least 148 papers between 1995 and 2018.

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Awards

IEEE Fellow

IEEE Fellow 2009, "For contributions to information processing and machine learning".

Timeline

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Bibliography

2018
Inference of the human polyadenylation code.
Bioinformatics, 2018

COSSMO: predicting competitive alternative splice site selection using deep learning.
Bioinformatics, 2018

2017
Generating and designing DNA with deep generative models.
CoRR, 2017

PixelGAN Autoencoders.
CoRR, 2017

Min-Max Propagation.
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017

PixelGAN Autoencoders.
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017

2016
Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets.
Proceedings of the IEEE, 2016

Are Random Forests Truly the Best Classifiers?
Journal of Machine Learning Research, 2016

Classifying and segmenting microscopy images with deep multiple instance learning.
Bioinformatics, 2016

Survey Propagation beyond Constraint Satisfaction Problems.
Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, 2016

2015
Classifying and Segmenting Microscopy Images Using Convolutional Multiple Instance Learning.
CoRR, 2015

Learning Wake-Sleep Recurrent Attention Models.
CoRR, 2015

Winner-Take-All Autoencoders.
Proceedings of the Advances in Neural Information Processing Systems 28: Annual Conference on Neural Information Processing Systems 2015, 2015

Learning Wake-Sleep Recurrent Attention Models.
Proceedings of the Advances in Neural Information Processing Systems 28: Annual Conference on Neural Information Processing Systems 2015, 2015

2014
Training Restricted Boltzmann Machine by Perturbation.
CoRR, 2014

A Winner-Take-All Method for Training Sparse Convolutional Autoencoders.
CoRR, 2014

Deep learning of the tissue-regulated splicing code.
Bioinformatics, 2014

Min-Max Problems on Factor Graphs.
Proceedings of the 31th International Conference on Machine Learning, 2014

2013
Bayesian Painting by Numbers: Flexible Priors for Colour-Invariant Object Recognition.
Proceedings of the Machine Learning for Computer Vision, 2013

A compendium of RNA-binding motifs for decoding gene regulation.
Nature, 2013

Variational Learning in Mixed-State Dynamic Graphical Models
CoRR, 2013

Learning Graphical Models of Images, Videos and Their Spatial Transformations
CoRR, 2013

A Factorized Variational Technique for Phase Unwrapping in Markov Random Fields
CoRR, 2013

k-Sparse Autoencoders.
CoRR, 2013

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry.
Bioinformatics, 2013

Adaptive dropout for training deep neural networks.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013

2012
Learning Generative Models of Similarity Matrices
CoRR, 2012

Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models
CoRR, 2012

Fast Exact Inference for Recursive Cardinality Models
CoRR, 2012

Convolutional Factor Graphs as Probabilistic Models
CoRR, 2012

Flexible Priors for Exemplar-based Clustering
CoRR, 2012

Cumulative distribution networks and the derivative-sum-product algorithm
CoRR, 2012

Hierarchical Affinity Propagation
CoRR, 2012

Matrix Tile Analysis.
CoRR, 2012

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data.
BMC Bioinformatics, 2012

Fast Exact Inference for Recursive Cardinality Models.
Proceedings of the Twenty-Eighth Conference on Uncertainty in Artificial Intelligence, 2012

Probabilistic n-Choose-k Models for Classification and Ranking.
Proceedings of the Advances in Neural Information Processing Systems 25: 26th Annual Conference on Neural Information Processing Systems 2012. Proceedings of a meeting held December 3-6, 2012

Factorizing appearance using epitomic flobject analysis.
Proceedings of the 2012 IEEE Conference on Computer Vision and Pattern Recognition, 2012

Learning structural element patch models with hierarchical palettes.
Proceedings of the 2012 IEEE Conference on Computer Vision and Pattern Recognition, 2012

2011
Cumulative Distribution Networks and the Derivative-sum-product Algorithm: Models and Inference for Cumulative Distribution Functions on Graphs.
Journal of Machine Learning Research, 2011

Interpreting Graph Cuts as a Max-Product Algorithm
CoRR, 2011

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.
Bioinformatics, 2011

Computational refinement of post-translational modifications predicted from tandem mass spectrometry.
Bioinformatics, 2011

Graph Cuts is a Max-Product Algorithm.
Proceedings of the UAI 2011, 2011

Hierarchical Affinity Propagation.
Proceedings of the UAI 2011, 2011

Learning better image representations using 'flobject analysis'.
Proceedings of the 24th IEEE Conference on Computer Vision and Pattern Recognition, 2011

STORMSeq: A Method for Ranking Regulatory Sequences by Integrating Experimental Datasets with Diverse Computational Predictions.
Proceedings of the Handbook of Statistical Bioinformatics., 2011

2010
Deciphering the splicing code.
Nature, 2010

Solving the Uncapacitated Facility Location Problem Using Message Passing Algorithms.
Proceedings of the Thirteenth International Conference on Artificial Intelligence and Statistics, 2010

Model-based detection of alternative splicing signals.
Bioinformatics [ISMB], 2010

2009
Rateless coding for arbitrary channel mixtures with decoder channel state information.
IEEE Trans. Information Theory, 2009

A Binary Variable Model for Affinity Propagation.
Neural Computation, 2009

Semi-Supervised Affinity Propagation with Instance-Level Constraints.
Proceedings of the Twelfth International Conference on Artificial Intelligence and Statistics, 2009

FLoSS: Facility location for subspace segmentation.
Proceedings of the IEEE 12th International Conference on Computer Vision, ICCV 2009, Kyoto, Japan, September 27, 2009

Stel component analysis: Modeling spatial correlations in image class structure.
Proceedings of the 2009 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2009), 2009

2008
Fast Transformation-Invariant Component Analysis.
International Journal of Computer Vision, 2008

Video Epitomes.
International Journal of Computer Vision, 2008

Flexible Priors for Exemplar-based Clustering.
Proceedings of the UAI 2008, 2008

Cumulative distribution networks and the derivative-sum-product algorithm.
Proceedings of the UAI 2008, 2008

Constructing Treatment Portfolios Using Affinity Propagation.
Proceedings of the Research in Computational Molecular Biology, 2008

Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3.
Proceedings of the Biocomputing 2008, 2008

Structured ranking learning using cumulative distribution networks.
Proceedings of the Advances in Neural Information Processing Systems 21, 2008

2007
Variational Probabilistic Speech Separation Using Microphone Arrays.
IEEE Trans. Audio, Speech & Language Processing, 2007

Bayesian Inference of MicroRNA Targets from Sequence and Expression Data.
Journal of Computational Biology, 2007

A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements.
Proceedings of the Research in Computational Molecular Biology, 2007

Learning in Biomedicine and Bioinformatics Using Affinity Propagation.
Proceedings of the Sixth International Conference on Machine Learning and Applications, 2007

Non-metric affinity propagation for unsupervised image categorization.
Proceedings of the IEEE 11th International Conference on Computer Vision, 2007

2006
Unwrapping of MR phase images using a Markov random field model.
IEEE Trans. Med. Imaging, 2006

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data.
Journal of Computational Biology, 2006

Inferring global levels of alternative splicing isoforms using a generative model of microarray data.
Bioinformatics, 2006

Matrix Tile Analysis.
Proceedings of the UAI '06, 2006

Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data.
Proceedings of the Research in Computational Molecular Biology, 2006

2005
A Comparison of Algorithms for Inference and Learning in Probabilistic Graphical Models.
IEEE Trans. Pattern Anal. Mach. Intell., 2005

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model.
Proceedings of the Research in Computational Molecular Biology, 2005

GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data.
Proceedings of the Biocomputing 2005, 2005

Using epitomes to model genetic diversity: Rational design of HIV vaccines.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005

Mixture Modeling by Affinity Propagation.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Multi-way clustering of microarray data using probabilistic sparse matrix factorization.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

A segment based probabilistic generative model of speech.
Proceedings of the 2005 IEEE International Conference on Acoustics, 2005

Video Epitomes.
Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2005), 2005

Variational Speech Separation of More Sources than Mixtures.
Proceedings of the Tenth International Workshop on Artificial Intelligence and Statistics, 2005

Generative Model for Layers of Appearance and Deformation.
Proceedings of the Tenth International Workshop on Artificial Intelligence and Statistics, 2005

2004
Convolutional Factor Graphs as Probabilistic Models.
Proceedings of the UAI '04, 2004

A Generative Model of Dense Optical Flow in Layers.
Proceedings of the Spatial Coherence for Visual Motion Analysis, 2004

Probabilistic Inference of Alternative Splicing Events in Microarray Data.
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004

Learning to cluster using local neighborhood structure.
Proceedings of the Machine Learning, 2004

2003
Transformation-Invariant Clustering Using the EM Algorithm.
IEEE Trans. Pattern Anal. Mach. Intell., 2003

Learning Generative Models of Similarity Matrices.
Proceedings of the UAI '03, 2003

Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models.
Proceedings of the UAI '03, 2003

Denoising and Untangling Graphs Using Degree Priors.
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003

Probabilistic Inference of Speech Signals from Phaseless Spectrograms.
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003

Robust variational speech separation using fewer microphones than speakers.
Proceedings of the 2003 IEEE International Conference on Multimedia and Expo, 2003

Multibaseline InSAR terrain elevation estimation: a dynamic programming approach.
Proceedings of the 2003 International Conference on Image Processing, 2003

Unsupervised Image Translation.
Proceedings of the 9th IEEE International Conference on Computer Vision (ICCV 2003), 2003

Epitomic analysis of appearance and shape.
Proceedings of the 9th IEEE International Conference on Computer Vision (ICCV 2003), 2003

Robust variational speech separation using fewer microphones than speakers.
Proceedings of the 2003 IEEE International Conference on Acoustics, 2003

Learning Appearance and Transparency Manifolds of Occluded Objects in Layers.
Proceedings of the 2003 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2003), 2003

Real-time On-line Learning of Transformed Hidden Markov Models from Video.
Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics, 2003

2002
Fast Transformation-Invariant Factor Analysis.
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002

Combination of statistical and rule-based approaches for spoken language understanding.
Proceedings of the 7th International Conference on Spoken Language Processing, ICSLP2002, 2002

An iterative dynamic programming approach to 2-D phase unwrapping.
Proceedings of the 2002 International Conference on Image Processing, 2002

Noise robust speech recognition using Gaussian basis functions for non-linear likelihood function approximation.
Proceedings of the IEEE International Conference on Acoustics, 2002

Accounting for uncertainity in observations: A new paradigm for Robust Automatic Speech Recognition.
Proceedings of the IEEE International Conference on Acoustics, 2002

Learning Montages of Transformed Latent Images as Representations of Objects That Change in Appearance.
Proceedings of the Computer Vision, 2002

2001
Factor graphs and the sum-product algorithm.
IEEE Trans. Information Theory, 2001

Signal-space characterization of iterative decoding.
IEEE Trans. Information Theory, 2001

Introduction to the special issue on codes on graphs and iterative algorithms.
IEEE Trans. Information Theory, 2001

A Factorized Variational Technique for Phase Unwrapping in Markov Random Field.
Proceedings of the UAI '01: Proceedings of the 17th Conference in Uncertainty in Artificial Intelligence, 2001

Very loopy belief propagation for unwrapping phase images.
Proceedings of the Advances in Neural Information Processing Systems 14 [Neural Information Processing Systems: Natural and Synthetic, 2001

Product Analysis: Learning to Model Observations as Products of Hidden Variables.
Proceedings of the Advances in Neural Information Processing Systems 14 [Neural Information Processing Systems: Natural and Synthetic, 2001

ALGONQUIN - Learning Dynamic Noise Models From Noisy Speech for Robust Speech Recognition.
Proceedings of the Advances in Neural Information Processing Systems 14 [Neural Information Processing Systems: Natural and Synthetic, 2001

Fast, Large-Scale Transformation-Invariant Clustering.
Proceedings of the Advances in Neural Information Processing Systems 14 [Neural Information Processing Systems: Natural and Synthetic, 2001

ALGONQUIN: iterating laplace's method to remove multiple types of acoustic distortion for robust speech recognition.
Proceedings of the EUROSPEECH 2001 Scandinavia, 2001

Separating Appearance from Deformation.
ICCV, 2001

Towards non-stationary model-based noise adaptation for large vocabulary speech recognition.
Proceedings of the IEEE International Conference on Acoustics, 2001

Unwrapping phase images by propagating probabilities across graphs.
Proceedings of the IEEE International Conference on Acoustics, 2001

Unwrapping phases by relaxed mean field inference.
Proceedings of the IEEE International Conference on Acoustics, 2001

Enforcing Integrability for Surface Reconstruction Algorithms Using Belief Propagation in Graphical Models.
Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2001), 2001

Learning Flexible Sprites in Video Layers.
Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2001), 2001

Learning mixtures of smooth, nonuniform deformation models for probabilistic image matching.
Proceedings of the Eighth International Workshop on Artificial Intelligence and Statistics, 2001

2000
Learning Graphical Models of Images, Videos and Their Spatial Transformations.
Proceedings of the UAI '00: Proceedings of the 16th Conference in Uncertainty in Artificial Intelligence, Stanford University, Stanford, California, USA, June 30, 2000

Keeping Flexible Active Contours on Track using Metropolis Updates.
Proceedings of the Advances in Neural Information Processing Systems 13, 2000

Sequentially Fitting "Inclusive" Trees for Inference in Noisy-OR Networks.
Proceedings of the Advances in Neural Information Processing Systems 13, 2000

Accumulator Networks: Suitors of Local Probability Propagation.
Proceedings of the Advances in Neural Information Processing Systems 13, 2000

Learning Sparse Multiple Cause Models.
Proceedings of the 15th International Conference on Pattern Recognition, 2000

Event-Coupled Hidden Markov Models.
Proceedings of the 2000 IEEE International Conference on Multimedia and Expo, 2000

Transformed Hidden Markov Models: Estimating Mixture Models of Images and Inferring Spatial Transformations in Video Sequence.
Proceedings of the 2000 Conference on Computer Vision and Pattern Recognition (CVPR 2000), 2000

Filling In Scenes by Propagating Probabilities through Layers and Into Appearance Models.
Proceedings of the 2000 Conference on Computer Vision and Pattern Recognition (CVPR 2000), 2000

1999
Variational Learning in Nonlinear Gaussian Belief Networks.
Neural Computation, 1999

Variational Learning in Mixed-State Dynamic Graphical Models.
Proceedings of the UAI '99: Proceedings of the Fifteenth Conference on Uncertainty in Artificial Intelligence, Stockholm, Sweden, July 30, 1999

Topographic Transformation as a Discrete Latent Variable.
Proceedings of the Advances in Neural Information Processing Systems 12, [NIPS Conference, Denver, Colorado, USA, November 29, 1999

Local Probability Propagation for Factor Analysis.
Proceedings of the Advances in Neural Information Processing Systems 12, [NIPS Conference, Denver, Colorado, USA, November 29, 1999

Detection and Tracking of Faces and Facial Features.
Proceedings of the 1999 International Conference on Image Processing, 1999

Embedded Face and Facial Expression Recognition.
Proceedings of the 1999 International Conference on Image Processing, 1999

Transformed Component Analysis: Joint Estimation of Spatial Transformations and Image Components.
ICCV, 1999

Time-Series Classification Using Mixed-State Dynamic Bayesian Networks.
Proceedings of the 1999 Conference on Computer Vision and Pattern Recognition (CVPR '99), 1999

Estimating Mixture Models of Images and Inferring Spatial Transformations Using the EM Algorithm.
Proceedings of the 1999 Conference on Computer Vision and Pattern Recognition (CVPR '99), 1999

A Probabilistic Framework for Embedded Face and Facial Expression Recognition.
Proceedings of the 1999 Conference on Computer Vision and Pattern Recognition (CVPR '99), 1999

1998
Iterative Decoding of Compound Codes by Probability Propagation in Graphical Models.
IEEE Journal on Selected Areas in Communications, 1998

Early Detection and Trellis Splicing: Reduced-Complexity Iterative Decoding.
IEEE Journal on Selected Areas in Communications, 1998

Probabalistic Multimedia Objects (Multijects): A Novel Approach to Video Indexing and Retrieval in Multimedia Systems.
Proceedings of the 1998 IEEE International Conference on Image Processing, 1998

Mixtures of Local Linear Subspaces for Face Recognition.
Proceedings of the 1998 Conference on Computer Vision and Pattern Recognition (CVPR '98), 1998

1997
Efficient Stochastic Source Coding and an Application to a Bayesian Network Source Model.
Comput. J., 1997

A Revolution: Belief Propagation in Graphs with Cycles.
Proceedings of the Advances in Neural Information Processing Systems 10, 1997

1996
Continuous Sigmoidal Belief Networks Trained using Slice Sampling.
Proceedings of the Advances in Neural Information Processing Systems 9, 1996

Free Energy Coding.
Proceedings of the 6th Data Compression Conference (DCC '96), Snowbird, Utah, USA, March 31, 1996

1995
Does the Wake-sleep Algorithm Produce Good Density Estimators?
Proceedings of the Advances in Neural Information Processing Systems 8, 1995


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