Does the Wake-sleep Algorithm Produce Good Density Estimators? - Brendan J. Frey; Geoffrey E. Hinton; Peter Dayan (NIPS, 1995)

Free Energy Coding. - Brendan J. Frey; Geoffrey E. Hinton (Data Compression Conference, 1996)

Continuous Sigmoidal Belief Networks Trained using Slice Sampling. - Brendan J. Frey (NIPS, 1996)

Variational Inference for continuous Sigmoidal Bayesian Networks. - Brendan J. Frey (AISTATS, 1997)

A Revolution: Belief Propagation in Graphs with Cycles. - Brendan J. Frey; David J. C. MacKay (NIPS, 1997)

Efficient Stochastic Source Coding and an Application to a Bayesian Network Source Model. - Brendan J. Frey; Geoffrey E. Hinton (Comput. J., 1997)

Mixtures of Local Linear Subspaces for Face Recognition. - Brendan J. Frey; Antonio Colmenarez; Thomas S. Huang (CVPR, 1998)

Probabalistic Multimedia Objects (Multijects): A Novel Approach to Video Indexing and Retrieval in Multimedia Systems. - Milind R. Naphade; Trausti T. Kristjansson; Brendan J. Frey; Thomas S. Huang (ICIP (3), 1998)

Early Detection and Trellis Splicing: Reduced-Complexity Iterative Decoding. - Brendan J. Frey; Frank R. Kschischang (IEEE J. Sel. Areas Commun., 1998)

Iterative Decoding of Compound Codes by Probability Propagation in Graphical Models. - Frank R. Kschischang; Brendan J. Frey (IEEE J. Sel. Areas Commun., 1998)

A Probabilistic Framework for Embedded Face and Facial Expression Recognition. - Antonio Colmenarez; Brendan J. Frey; Thomas S. Huang (CVPR, 1999)

Estimating Mixture Models of Images and Inferring Spatial Transformations Using the EM Algorithm. - Brendan J. Frey; Nebojsa Jojic (CVPR, 1999)

Time-Series Classification Using Mixed-State Dynamic Bayesian Networks. - Vladimir Pavlovic 001; Brendan J. Frey; Thomas S. Huang (CVPR, 1999)

Transformed Component Analysis: Joint Estimation of Spatial Transformations and Image Components. - Brendan J. Frey; Nebojsa Jojic (ICCV, 1999)

Embedded Face and Facial Expression Recognition. - Antonio Colmenarez; Brendan J. Frey; Thomas S. Huang (ICIP (1), 1999)

Detection and Tracking of Faces and Facial Features. - Antonio Colmenarez; Brendan J. Frey; Thomas S. Huang (ICIP (1), 1999)

Local Probability Propagation for Factor Analysis. - Brendan J. Frey (NIPS, 1999)

Topographic Transformation as a Discrete Latent Variable. - Nebojsa Jojic; Brendan J. Frey (NIPS, 1999)

Variational Learning in Mixed-State Dynamic Graphical Models. - Vladimir Pavlovic 001; Brendan J. Frey; Thomas S. Huang (UAI, 1999)

Variational Learning in Nonlinear Gaussian Belief Networks. - Brendan J. Frey; Geoffrey E. Hinton (Neural Comput., 1999)

Filling In Scenes by Propagating Probabilities through Layers and Into Appearance Models. - Brendan J. Frey (CVPR, 2000)

Transformed Hidden Markov Models: Estimating Mixture Models of Images and Inferring Spatial Transformations in Video Sequence. - Nebojsa Jojic; Nemanja Petrovic; Thomas S. Huang; Brendan J. Frey (CVPR, 2000)

Event-Coupled Hidden Markov Models. - Trausti T. Kristjansson; Brendan J. Frey; Thomas S. Huang (IEEE International Conference on Multimedia and Expo (I), 2000)

Learning Sparse Multiple Cause Models. - Milind R. Naphade; Lawrence S. Chen; Thomas S. Huang; Brendan J. Frey (ICPR, 2000)

Accumulator Networks: Suitors of Local Probability Propagation. - Brendan J. Frey; Anitha Kannan (NIPS, 2000)

Sequentially Fitting "Inclusive" Trees for Inference in Noisy-OR Networks. - Brendan J. Frey; Relu Patrascu; Tommi S. Jaakkola; Jodi Moran (NIPS, 2000)

Keeping Flexible Active Contours on Track using Metropolis Updates. - Trausti T. Kristjansson; Brendan J. Frey (NIPS, 2000)

Learning Graphical Models of Images, Videos and Their Spatial Transformations. - Brendan J. Frey; Nebojsa Jojic (UAI, 2000)

Learning mixtures of smooth, nonuniform deformation models for probabilistic image matching. - Nebojsa Jojic; Patrice Y. Simard; Brendan J. Frey; David Heckerman (AISTATS, 2001)

Learning Flexible Sprites in Video Layers. - Nebojsa Jojic; Brendan J. Frey (CVPR (1), 2001)

Enforcing Integrability for Surface Reconstruction Algorithms Using Belief Propagation in Graphical Models. - Nemanja Petrovic; Ira Cohen; Brendan J. Frey; Ralf Koetter; Thomas S. Huang (CVPR (1), 2001)

Unwrapping phases by relaxed mean field inference. - Kannan Achan; Brendan J. Frey; Ralf Koetter; David C. Munson Jr. (ICASSP, 2001)

Unwrapping phase images by propagating probabilities across graphs. - Ralf Koetter; Brendan J. Frey; Nemanja Petrovic; David C. Munson Jr. (ICASSP, 2001)

Towards non-stationary model-based noise adaptation for large vocabulary speech recognition. - Trausti T. Kristjansson; Brendan J. Frey; Li Deng 001; Alex Acero (ICASSP, 2001)

Separating Appearance from Deformation. - Nebojsa Jojic; Patrice Y. Simard; Brendan J. Frey; David Heckerman (ICCV, 2001)

ALGONQUIN: iterating laplace's method to remove multiple types of acoustic distortion for robust speech recognition. - Brendan J. Frey; Li Deng 001; Alex Acero; Trausti T. Kristjansson (INTERSPEECH, 2001)

"Codes" on images and iterative phase unwrapping. - Brendan J. Frey; Ralf Koetter; Nemanja Petrovic (ITW, 2001)

Fast, Large-Scale Transformation-Invariant Clustering. - Brendan J. Frey; Nebojsa Jojic (NIPS, 2001)

ALGONQUIN - Learning Dynamic Noise Models From Noisy Speech for Robust Speech Recognition. - Brendan J. Frey; Trausti T. Kristjansson; Li Deng 001; Alex Acero (NIPS, 2001)

Product Analysis: Learning to Model Observations as Products of Hidden Variables. - Brendan J. Frey; Anitha Kannan; Nebojsa Jojic (NIPS, 2001)

Very loopy belief propagation for unwrapping phase images. - Brendan J. Frey; Ralf Koetter; Nemanja Petrovic (NIPS, 2001)

A Factorized Variational Technique for Phase Unwrapping in Markov Random Field. - Kannan Achan; Brendan J. Frey; Ralf Koetter (UAI, 2001)

Introduction to the special issue on codes on graphs and iterative algorithms. - Brendan J. Frey; Ralf Koetter; G. David Forney Jr.; Frank R. Kschischang; Robert J. McEliece; Daniel A. Spielman (IEEE Trans. Inf. Theory, 2001)

Signal-space characterization of iterative decoding. - Brendan J. Frey; Ralf Koetter; Alexander Vardy (IEEE Trans. Inf. Theory, 2001)

Factor graphs and the sum-product algorithm. - Frank R. Kschischang; Brendan J. Frey; Hans-Andrea Loeliger (IEEE Trans. Inf. Theory, 2001)

Learning Montages of Transformed Latent Images as Representations of Objects That Change in Appearance. - Chris Pal; Brendan J. Frey; Nebojsa Jojic (ECCV (4), 2002)

Accounting for uncertainity in observations: A new paradigm for Robust Automatic Speech Recognition. - Trausti T. Kristjansson; Brendan J. Frey (ICASSP, 2002)

Noise robust speech recognition using Gaussian basis functions for non-linear likelihood function approximation. - Chris Pal; Brendan J. Frey; Trausti T. Kristjansson (ICASSP, 2002)

Phase unwrapping by minimizing Kikuchi free energy. - Kannan Achan; Brendan J. Frey; Ralf Koetter; David C. Munson (IGARSS, 2002)

Balancing rewrapping error and smoothness in two dimensional phase unwrapping problems. - David C. Schultz; Ralf Koetter; Brendan J. Frey; David C. Munson Jr. (IGARSS, 2002)

An iterative dynamic programming approach to 2-D phase unwrapping. - Lei Ying 005; Brendan J. Frey; Ralf Koetter; David C. Munson (IGARSS, 2002)

Combination of statistical and rule-based approaches for spoken language understanding. - Ye-Yi Wang; Alex Acero; Ciprian Chelba; Brendan J. Frey; Leon Wong (INTERSPEECH, 2002)

Fast Transformation-Invariant Factor Analysis. - Anitha Kannan; Nebojsa Jojic; Brendan J. Frey (NIPS, 2002)

Real-time On-line Learning of Transformed Hidden Markov Models from Video. - Nemanja Petrovic; Nebojsa Jojic; Brendan J. Frey; Thomas S. Huang (AISTATS, 2003)

Learning Appearance and Transparency Manifolds of Occluded Objects in Layers. - Brendan J. Frey; Nebojsa Jojic; Anitha Kannan (CVPR (1), 2003)

Robust variational speech separation using fewer microphones than speakers. - Steven J. Rennie; Parham Aarabi; Trausti T. Kristjansson; Brendan J. Frey; Kannan Achan (ICASSP (1), 2003)

Epitomic analysis of appearance and shape. - Nebojsa Jojic; Brendan J. Frey; Anitha Kannan (ICCV, 2003)

Unsupervised Image Translation. - Rómer Rosales; Kannan Achan; Brendan J. Frey (ICCV, 2003)

Multibaseline InSAR terrain elevation estimation: a dynamic programming approach. - Lei Ying 001; David C. Munson; Ralf Koetter; Brendan J. Frey (ICIP (3), 2003)

Probabilistic Inference of Speech Signals from Phaseless Spectrograms. - Kannan Achan; Sam T. Roweis; Brendan J. Frey (NIPS, 2003)

Denoising and Untangling Graphs Using Degree Priors. - Quaid Morris; Brendan J. Frey (NIPS, 2003)

Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models. - Brendan J. Frey (UAI, 2003)

Learning Generative Models of Similarity Matrices. - Rómer Rosales; Brendan J. Frey (UAI, 2003)

Transformation-Invariant Clustering Using the EM Algorithm. - Brendan J. Frey; Nebojsa Jojic (IEEE Trans. Pattern Anal. Mach. Intell., 2003)

Learning to cluster using local neighborhood structure. - Rómer Rosales; Kannan Achan; Brendan J. Frey (ICML, 2004)

On interacting encoders and decoders in multiuser settings. - Stark C. Draper; Brendan J. Frey; Frank R. Kschischang (ISIT, 2004)

Efficient variable length channel coding for unknown DMCs. - Stark C. Draper; Brendan J. Frey; Frank R. Kschischang (ISIT, 2004)

Probabilistic Inference of Alternative Splicing Events in Microarray Data. - Ofer Shai; Brendan J. Frey; Quaid Morris; Qun Pan 001; Christine Misquitta; Benjamin J. Blencowe (NIPS, 2004)

A Generative Model of Dense Optical Flow in Layers. - Anitha Kannan; Brendan J. Frey; Nebojsa Jojic (SCVMA, 2004)

Convolutional Factor Graphs as Probabilistic Models. - Yongyi Mao; Frank R. Kschischang; Brendan J. Frey (UAI, 2004)

Generative Model for Layers of Appearance and Deformation. - Anitha Kannan; Nebojsa Jojic; Brendan J. Frey (AISTATS, 2005)

Variational Speech Separation of More Sources than Mixtures. - Steven J. Rennie; Kannan Achan; Brendan J. Frey; Parham Aarabi (AISTATS, 2005)

A segment based probabilistic generative model of speech. - Kannan Achan; Sam T. Roweis; Aaron Hertzmann; Brendan J. Frey (ICASSP (5), 2005)

Multi-way clustering of microarray data using probabilistic sparse matrix factorization. - Delbert Dueck; Quaid Morris; Brendan J. Frey (ISMB (Supplement of Bioinformatics), 2005)

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. - Jim C. Huang; Quaid Morris; Timothy R. Hughes; Brendan J. Frey (ISMB (Supplement of Bioinformatics), 2005)

Mixture Modeling by Affinity Propagation. - Brendan J. Frey; Delbert Dueck (NIPS, 2005)

Using epitomes to model genetic diversity: Rational design of HIV vaccines. - Nebojsa Jojic; Vladimir Jojic; Brendan J. Frey; Christopher Meek; David Heckerman (NIPS, 2005)

GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data. - Brendan J. Frey; Quaid Morris; Wen Zhang; Naveed Mohammad; Timothy R. Hughes (Pacific Symposium on Biocomputing, 2005)

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. - Brendan J. Frey; Quaid Morris; Mark D. Robinson; Timothy R. Hughes (RECOMB, 2005)

A Comparison of Algorithms for Inference and Learning in Probabilistic Graphical Models. - Brendan J. Frey; Nebojsa Jojic (IEEE Trans. Pattern Anal. Mach. Intell., 2005)

Beyond genomics: Detecting codes and signals in the cellular transcriptome [Plenary speakers]. - Brendan J. Frey (ISIT, 2006)

Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. - Jim C. Huang; Quaid Morris; Brendan J. Frey (RECOMB, 2006)

Matrix Tile Analysis. - Inmar E. Givoni; Vincent Cheung; Brendan J. Frey (UAI, 2006)

Inferring global levels of alternative splicing isoforms using a generative model of microarray data. - Ofer Shai; Quaid Morris; Benjamin J. Blencowe; Brendan J. Frey (Bioinform., 2006)

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data. - Brendan J. Frey; Quaid Morris; Timothy R. Hughes (J. Comput. Biol., 2006)

Unwrapping of MR phase images using a Markov random field model. - Lei Ying 001; Zhi-Pei Liang; David C. Munson; Ralf Koetter; Brendan J. Frey (IEEE Trans. Medical Imaging, 2006)

Non-metric affinity propagation for unsupervised image categorization. - Delbert Dueck; Brendan J. Frey (ICCV, 2007)

Learning in Biomedicine and Bioinformatics Using Affinity Propagation. - Brendan J. Frey (ICMLA, 2007)

A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements. - Anitha Kannan; Andrew Emili; Brendan J. Frey (RECOMB, 2007)

Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. - Jim C. Huang; Quaid Morris; Brendan J. Frey (J. Comput. Biol., 2007)

Variational Probabilistic Speech Separation Using Microphone Arrays. - Steven J. Rennie; Parham Aarabi; Brendan J. Frey (IEEE Trans. Speech Audio Process., 2007)

Structured ranking learning using cumulative distribution networks. - Jim C. Huang; Brendan J. Frey (NIPS, 2008)

Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. - Jim C. Huang; Brendan J. Frey; Quaid Morris (Pacific Symposium on Biocomputing, 2008)

Constructing Treatment Portfolios Using Affinity Propagation. - Delbert Dueck; Brendan J. Frey; Nebojsa Jojic; Vladimir Jojic; Guri Giaever; Andrew Emili; Gabe Musso; Robert Hegele (RECOMB, 2008)

Cumulative distribution networks and the derivative-sum-product algorithm. - Jim C. Huang; Brendan J. Frey (UAI, 2008)

Flexible Priors for Exemplar-based Clustering. - Daniel Tarlow; Richard S. Zemel; Brendan J. Frey (UAI, 2008)

Video Epitomes. - Vincent Cheung; Brendan J. Frey; Nebojsa Jojic (Int. J. Comput. Vis., 2008)

Fast Transformation-Invariant Component Analysis. - Anitha Kannan; Nebojsa Jojic; Brendan J. Frey (Int. J. Comput. Vis., 2008)

Stel component analysis: Modeling spatial correlations in image class structure. - Nebojsa Jojic; Alessandro Perina; Marco Cristani; Vittorio Murino; Brendan J. Frey (CVPR, 2009)

FLoSS: Facility location for subspace segmentation. - Nevena Lazic; Inmar E. Givoni; Brendan J. Frey; Parham Aarabi (ICCV, 2009)

Semi-Supervised Affinity Propagation with Instance-Level Constraints. - Inmar E. Givoni; Brendan J. Frey (AISTATS, 2009)

A Binary Variable Model for Affinity Propagation. - Inmar E. Givoni; Brendan J. Frey (Neural Comput., 2009)

Rateless coding for arbitrary channel mixtures with decoder channel state information. - Stark C. Draper; Frank R. Kschischang; Brendan J. Frey (IEEE Trans. Inf. Theory, 2009)

Model-based detection of alternative splicing signals. - Yoseph Barash; Benjamin J. Blencowe; Brendan J. Frey (Bioinform., 2010)

Solving the Uncapacitated Facility Location Problem Using Message Passing Algorithms. - Nevena Lazic; Brendan J. Frey; Parham Aarabi (AISTATS, 2010)

Deciphering the splicing code. - Yoseph Barash; John A. Calarco; Weijun Gao; Qun Pan 001; Xinchen Wang; Ofer Shai; Benjamin J. Blencowe; Brendan J. Frey (Nat., 2010)

STORMSeq: A Method for Ranking Regulatory Sequences by Integrating Experimental Datasets with Diverse Computational Predictions. - Jim C. Huang; Brendan J. Frey (Handbook of Statistical Bioinformatics, 2011)

Learning better image representations using 'flobject analysis'. - Patrick S. Li; Inmar E. Givoni; Brendan J. Frey (CVPR, 2011)

Hierarchical Affinity Propagation. - Inmar E. Givoni; Clement Chung; Brendan J. Frey (UAI, 2011)

Graph Cuts is a Max-Product Algorithm. - Daniel Tarlow; Inmar E. Givoni; Richard S. Zemel; Brendan J. Frey (UAI, 2011)

Computational refinement of post-translational modifications predicted from tandem mass spectrometry. - Clement Chung; Jian Liu; Andrew Emili; Brendan J. Frey (Bioinform., 2011)

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context. - Hui Yuan Xiong; Yoseph Barash; Brendan J. Frey (Bioinform., 2011)

Interpreting Graph Cuts as a Max-Product Algorithm - Daniel Tarlow; Inmar E. Givoni; Richard S. Zemel; Brendan J. Frey (CoRR, 2011)

Cumulative Distribution Networks and the Derivative-sum-product Algorithm: Models and Inference for Cumulative Distribution Functions on Graphs. - Jim C. Huang; Brendan J. Frey (J. Mach. Learn. Res., 2011)

Learning structural element patch models with hierarchical palettes. - Jeroen Chua; Inmar E. Givoni; Ryan Prescott Adams; Brendan J. Frey (CVPR, 2012)

Factorizing appearance using epitomic flobject analysis. - Patrick S. Li; Brendan J. Frey (CVPR, 2012)

Probabilistic n-Choose-k Models for Classification and Ranking. - Kevin Swersky; Daniel Tarlow; Ryan P. Adams; Richard S. Zemel; Brendan J. Frey (NIPS, 2012)

Fast Exact Inference for Recursive Cardinality Models. - Daniel Tarlow; Kevin Swersky; Richard S. Zemel; Ryan Prescott Adams; Brendan J. Frey (UAI, 2012)

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. - Boyko Kakaradov; Hui Yuan Xiong; Leo J. Lee; Nebojsa Jojic; Brendan J. Frey (BMC Bioinform., 2012)

Adaptive dropout for training deep neural networks. - Lei Jimmy Ba; Brendan J. Frey (NIPS, 2013)

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. - Clement Chung; Andrew Emili; Brendan J. Frey (Bioinform., 2013)

A Factorized Variational Technique for Phase Unwrapping in Markov Random Fields - Kannan Achan; Brendan J. Frey; Ralf Koetter (CoRR, 2013)

A compendium of RNA-binding motifs for decoding gene regulation. - Debashish Ray; Hilal Kazan; Kate B. Cook; Matthew T. Weirauch; Hamed S. Najafabadi; Xiao Li; Serge Gueroussov; Mihai Albu; Hong Zheng; Ally Yang; Hong Na; Manuel Irimia; et al. (Nat., 2013)

Bayesian Painting by Numbers: Flexible Priors for Colour-Invariant Object Recognition. - Jeroen C. Chua; Inmar E. Givoni; Ryan P. Adams; Brendan J. Frey (Machine Learning for Computer Vision, 2013)

Min-Max Problems on Factor Graphs. - Siamak Ravanbakhsh; Christopher Srinivasa; Brendan J. Frey; Russell Greiner (ICML, 2014)

Deep learning of the tissue-regulated splicing code. - Michael K. K. Leung; Hui Yuan Xiong; Leo J. Lee; Brendan J. Frey (Bioinform., 2014)

k-Sparse Autoencoders. - Alireza Makhzani; Brendan J. Frey (ICLR (Poster), 2014)

A Winner-Take-All Method for Training Sparse Convolutional Autoencoders. - Alireza Makhzani; Brendan J. Frey (CoRR, 2014)

Training Restricted Boltzmann Machine by Perturbation. - Siamak Ravanbakhsh; Russell Greiner; Brendan J. Frey (CoRR, 2014)

Learning Wake-Sleep Recurrent Attention Models. - Jimmy Ba; Ruslan Salakhutdinov; Roger B. Grosse; Brendan J. Frey (NIPS, 2015)

Winner-Take-All Autoencoders. - Alireza Makhzani; Brendan J. Frey (NIPS, 2015)

Classifying and Segmenting Microscopy Images Using Convolutional Multiple Instance Learning. - Oren Z. Kraus; Lei Jimmy Ba; Brendan J. Frey (CoRR, 2015)

Survey Propagation beyond Constraint Satisfaction Problems. - Christopher Srinivasa; Siamak Ravanbakhsh; Brendan J. Frey (AISTATS, 2016)

Classifying and segmenting microscopy images with deep multiple instance learning. - Oren Z. Kraus; Lei Jimmy Ba; Brendan J. Frey (Bioinform., 2016)

Are Random Forests Truly the Best Classifiers? - Michael Wainberg; Babak Alipanahi; Brendan J. Frey (J. Mach. Learn. Res., 2016)

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets. - Michael K. K. Leung; Andrew Delong; Babak Alipanahi; Brendan J. Frey (Proc. IEEE, 2016)

PixelGAN Autoencoders. - Alireza Makhzani; Brendan J. Frey (NIPS, 2017)

Min-Max Propagation. - Christopher Srinivasa; Inmar E. Givoni; Siamak Ravanbakhsh; Brendan J. Frey (NIPS, 2017)

Generating and designing DNA with deep generative models. - Nathan Killoran; Leo J. Lee; Andrew Delong; David Duvenaud; Brendan J. Frey (CoRR, 2017)

COSSMO: predicting competitive alternative splice site selection using deep learning. - Hannes Bretschneider; Shreshth Gandhi; Amit G. Deshwar; Khalid Zuberi; Brendan J. Frey (Bioinform., 2018)

Inference of the human polyadenylation code. - Michael K. K. Leung; Andrew Delong; Brendan J. Frey (Bioinform., 2018)

A graph neural network approach for molecule carcinogenicity prediction. - Philip Fradkin; Adamo Young; Lazar Atanackovic; Brendan J. Frey; Leo J. Lee; Bo Wang 044 (Bioinform., 2022)

Splicing Up Your Predictions with RNA Contrastive Learning. - Philip Fradkin; Ruian Shi; Bo Wang 044; Brendan J. Frey; Leo J. Lee (CoRR, 2023)