| 2017 | RECOMB | Inference of the Human Polyadenylation Code. | Michael K. K. Leung, Andrew Delong, Brendan J. Frey |
| 2016 | AISTATS | Survey Propagation beyond Constraint Satisfaction Problems. | Christopher Srinivasa, Siamak Ravanbakhsh, Brendan J. Frey |
| 2014 | ICML | Min-Max Problems on Factor Graphs. | Siamak Ravanbakhsh, Christopher Srinivasa, Brendan J. Frey, Russell Greiner |
| 2012 | CVPR | Learning structural element patch models with hierarchical palettes. | Jeroen Chua, Inmar E. Givoni, Ryan Prescott Adams, Brendan J. Frey |
| 2012 | CVPR | Factorizing appearance using epitomic flobject analysis. | Patrick S. Li, Brendan J. Frey |
| 2012 | UAI | Fast Exact Inference for Recursive Cardinality Models. | Daniel Tarlow, Kevin Swersky, Richard S. Zemel, Ryan Prescott Adams, Brendan J. Frey |
| 2011 | CVPR | Learning better image representations using 'flobject analysis'. | Patrick S. Li, Inmar E. Givoni, Brendan J. Frey |
| 2011 | UAI | Hierarchical Affinity Propagation. | Inmar E. Givoni, Clement Chung, Brendan J. Frey |
| 2011 | UAI | Graph Cuts is a Max-Product Algorithm. | Daniel Tarlow, Inmar E. Givoni, Richard S. Zemel, Brendan J. Frey |
| 2009 | CVPR | Stel component analysis: Modeling spatial correlations in image class structure. | Nebojsa Jojic, Alessandro Perina, Marco Cristani, Vittorio Murino, Brendan J. Frey |
| 2009 | ICCV | FLoSS: Facility location for subspace segmentation. | Nevena Lazic, Inmar E. Givoni, Brendan J. Frey, Parham Aarabi |
| 2008 | PSB | Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. | Jim C. Huang, Brendan J. Frey, Quaid Morris |
| 2008 | RECOMB | Constructing Treatment Portfolios Using Affinity Propagation. | Delbert Dueck, Brendan J. Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili, Gabe Musso, Robert Hegele |
| 2008 | UAI | Cumulative distribution networks and the derivative-sum-product algorithm. | Jim C. Huang, Brendan J. Frey |
| 2008 | UAI | Flexible Priors for Exemplar-based Clustering. | Daniel Tarlow, Richard S. Zemel, Brendan J. Frey |
| 2007 | ICCV | Non-metric affinity propagation for unsupervised image categorization. | Delbert Dueck, Brendan J. Frey |
| 2007 | ICMLA | Learning in Biomedicine and Bioinformatics Using Affinity Propagation. | Brendan J. Frey |
| 2007 | RECOMB | A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements. | Anitha Kannan, Andrew Emili, Brendan J. Frey |
| 2006 | ISIT | Beyond genomics: Detecting codes and signals in the cellular transcriptome [Plenary speakers]. | Brendan J. Frey |
| 2006 | RECOMB | Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. | Jim C. Huang, Quaid Morris, Brendan J. Frey |
| 2006 | UAI | Matrix Tile Analysis. | Inmar E. Givoni, Vincent Cheung, Brendan J. Frey |
| 2005 | AISTATS | Generative Model for Layers of Appearance and Deformation. | Anitha Kannan, Nebojsa Jojic, Brendan J. Frey |
| 2005 | AISTATS | Variational Speech Separation of More Sources than Mixtures. | Steven J. Rennie, Kannan Achan, Brendan J. Frey, Parham Aarabi |
| 2005 | CVPR | Video Epitomes. | Vincent Cheung, Brendan J. Frey, Nebojsa Jojic |
| 2005 | ICASSP | A segment based probabilistic generative model of speech. | Kannan Achan, Sam T. Roweis, Aaron Hertzmann, Brendan J. Frey |
| 2005 | ISMB | Multi-way clustering of microarray data using probabilistic sparse matrix factorization. | Delbert Dueck, Quaid Morris, Brendan J. Frey |
| 2005 | ISMB | 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 |
| 2005 | PSB | 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 |
| 2005 | RECOMB | 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 |
| 2004 | ICML | Learning to cluster using local neighborhood structure. | Rmer Rosales, Kannan Achan, Brendan J. Frey |
| 2004 | ISIT | On interacting encoders and decoders in multiuser settings. | Stark C. Draper, Brendan J. Frey, Frank R. Kschischang |
| 2004 | ISIT | Efficient variable length channel coding for unknown DMCs. | Stark C. Draper, Brendan J. Frey, Frank R. Kschischang |
| 2004 | UAI | Convolutional Factor Graphs as Probabilistic Models. | Yongyi Mao, Frank R. Kschischang, Brendan J. Frey |
| 2003 | AISTATS | Real-time On-line Learning of Transformed Hidden Markov Models from Video. | Nemanja Petrovic, Nebojsa Jojic, Brendan J. Frey, Thomas S. Huang |
| 2003 | CVPR | Learning Appearance and Transparency Manifolds of Occluded Objects in Layers. | Brendan J. Frey, Nebojsa Jojic, Anitha Kannan |
| 2003 | ICASSP | Robust variational speech separation using fewer microphones than speakers. | Steven J. Rennie, Parham Aarabi, Trausti T. Kristjansson, Brendan J. Frey, Kannan Achan |
| 2003 | ICCV | Epitomic analysis of appearance and shape. | Nebojsa Jojic, Brendan J. Frey, Anitha Kannan |
| 2003 | ICCV | Unsupervised Image Translation. | Rmer Rosales, Kannan Achan, Brendan J. Frey |
| 2003 | ICIP | Multibaseline InSAR terrain elevation estimation: a dynamic programming approach. | Lei Ying, David C. Munson, Ralf Koetter, Brendan J. Frey |
| 2003 | UAI | Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models. | Brendan J. Frey |
| 2003 | UAI | Learning Generative Models of Similarity Matrices. | Rmer Rosales, Brendan J. Frey |
| 2002 | ECCV | Learning Montages of Transformed Latent Images as Representations of Objects That Change in Appearance. | Chris Pal, Brendan J. Frey, Nebojsa Jojic |
| 2002 | ICASSP | Accounting for uncertainity in observations: A new paradigm for Robust Automatic Speech Recognition. | Trausti T. Kristjansson, Brendan J. Frey |
| 2002 | ICASSP | Noise robust speech recognition using Gaussian basis functions for non-linear likelihood function approximation. | Chris Pal, Brendan J. Frey, Trausti T. Kristjansson |
| 2002 | ICIP | An iterative dynamic programming approach to 2-D phase unwrapping. | Lei Ying, David C. Munson, Ralf Koetter, Brendan J. Frey |
| 2002 | IGARSS | Balancing rewrapping error and smoothness in two dimensional phase unwrapping problems. | David C. Schultz, Ralf Koetter, Brendan J. Frey, David C. Munson Jr. |
| 2002 | IGARSS | An iterative dynamic programming approach to 2-D phase unwrapping. | Lei Ying, Brendan J. Frey, Ralf Koetter, David C. Munson |
| 2002 | Interspeech | Combination of statistical and rule-based approaches for spoken language understanding. | Ye-Yi Wang, Alex Acero, Ciprian Chelba, Brendan J. Frey, Leon Wong |
| 2002 | IGARSS | Phase unwrapping by minimizing Kikuchi free energy. | Kannan Achan, Brendan J. Frey, Ralf Koetter, David C. Munson |
| 2001 | AISTATS | Learning mixtures of smooth, nonuniform deformation models for probabilistic image matching. | Nebojsa Jojic, Patrice Y. Simard, Brendan J. Frey, David Heckerman |
| 2001 | CVPR | Learning Flexible Sprites in Video Layers. | Nebojsa Jojic, Brendan J. Frey |
| 2001 | CVPR | Enforcing Integrability for Surface Reconstruction Algorithms Using Belief Propagation in Graphical Models. | Nemanja Petrovic, Ira Cohen, Brendan J. Frey, Ralf Koetter, Thomas S. Huang |
| 2001 | ICASSP | Unwrapping phases by relaxed mean field inference. | Kannan Achan, Brendan J. Frey, Ralf Koetter, David C. Munson Jr. |
| 2001 | ICASSP | Unwrapping phase images by propagating probabilities across graphs. | Ralf Koetter, Brendan J. Frey, Nemanja Petrovic, David C. Munson Jr. |
| 2001 | ICASSP | Towards non-stationary model-based noise adaptation for large vocabulary speech recognition. | Trausti T. Kristjansson, Brendan J. Frey, Li Deng, Alex Acero |
| 2001 | ICCV | Separating Appearance from Deformation. | Nebojsa Jojic, Patrice Y. Simard, Brendan J. Frey, David Heckerman |
| 2001 | Interspeech | ALGONQUIN: iterating laplace's method to remove multiple types of acoustic distortion for robust speech recognition. | Brendan J. Frey, Li Deng, Alex Acero, Trausti T. Kristjansson |
| 2001 | ITW | "Codes" on images and iterative phase unwrapping. | Brendan J. Frey, Ralf Koetter, Nemanja Petrovic |
| 2001 | UAI | A Factorized Variational Technique for Phase Unwrapping in Markov Random Field. | Kannan Achan, Brendan J. Frey, Ralf Koetter |
| 2000 | CVPR | Filling In Scenes by Propagating Probabilities through Layers and Into Appearance Models. | Brendan J. Frey |
| 2000 | CVPR | 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 |
| 2000 | ICPR | Learning Sparse Multiple Cause Models. | Milind R. Naphade, Lawrence S. Chen, Thomas S. Huang, Brendan J. Frey |
| 2000 | UAI | Learning Graphical Models of Images, Videos and Their Spatial Transformations. | Brendan J. Frey, Nebojsa Jojic |
| 1999 | CVPR | A Probabilistic Framework for Embedded Face and Facial Expression Recognition. | Antonio Colmenarez, Brendan J. Frey, Thomas S. Huang |
| 1999 | CVPR | Estimating Mixture Models of Images and Inferring Spatial Transformations Using the EM Algorithm. | Brendan J. Frey, Nebojsa Jojic |
| 1999 | CVPR | Time-Series Classification Using Mixed-State Dynamic Bayesian Networks. | Vladimir Pavlovic, Brendan J. Frey, Thomas S. Huang |
| 1999 | ICCV | Transformed Component Analysis: Joint Estimation of Spatial Transformations and Image Components. | Brendan J. Frey, Nebojsa Jojic |
| 1999 | ICIP | Embedded Face and Facial Expression Recognition. | Antonio Colmenarez, Brendan J. Frey, Thomas S. Huang |
| 1999 | ICIP | Detection and Tracking of Faces and Facial Features. | Antonio Colmenarez, Brendan J. Frey, Thomas S. Huang |
| 1999 | UAI | Variational Learning in Mixed-State Dynamic Graphical Models. | Vladimir Pavlovic, Brendan J. Frey, Thomas S. Huang |
| 1998 | CVPR | Mixtures of Local Linear Subspaces for Face Recognition. | Brendan J. Frey, Antonio Colmenarez, Thomas S. Huang |
| 1998 | ICIP | 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 |
| 1997 | AISTATS | Variational Inference for continuous Sigmoidal Bayesian Networks. | Brendan J. Frey |
| 1996 | DCC | Free Energy Coding. | Brendan J. Frey, Geoffrey E. Hinton |