Brendan J. Frey

Publication Activity (10 Years)

Years Active: 1995-2023
Publications (10 Years): 16

Top Venues

CoRR

Bioinform.

NIPS

AISTATS

Publications

Philip Fradkin, Ruian Shi, Bo Wang, Brendan J. Frey, Leo J. Lee
Splicing Up Your Predictions with RNA Contrastive Learning. CoRR (2023)
Hannes Bretschneider, Shreshth Gandhi, Amit G. Deshwar, Khalid Zuberi, Brendan J. Frey
COSSMO: predicting competitive alternative splice site selection using deep learning. Bioinform. 34 (13) (2018)
Michael K. K. Leung, Andrew Delong, Brendan J. Frey
Inference of the human polyadenylation code. Bioinform. 34 (17) (2018)
Michael K. K. Leung, Andrew Delong, Brendan J. Frey
Inference of the Human Polyadenylation Code. RECOMB (2017)
Alireza Makhzani, Brendan J. Frey
PixelGAN Autoencoders. NIPS (2017)
Alireza Makhzani, Brendan J. Frey
PixelGAN Autoencoders. CoRR (2017)
Christopher Srinivasa, Inmar E. Givoni, Siamak Ravanbakhsh, Brendan J. Frey
Min-Max Propagation. NIPS (2017)
Nathan Killoran, Leo J. Lee, Andrew Delong, David Duvenaud, Brendan J. Frey
Generating and designing DNA with deep generative models. CoRR (2017)
Christopher Srinivasa, Siamak Ravanbakhsh, Brendan J. Frey
Survey Propagation beyond Constraint Satisfaction Problems. AISTATS (2016)
Michael K. K. Leung, Andrew Delong, Babak Alipanahi, Brendan J. Frey
Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets. Proc. IEEE 104 (1) (2016)
Michael Wainberg, Babak Alipanahi, Brendan J. Frey
Are Random Forests Truly the Best Classifiers? J. Mach. Learn. Res. 17 (2016)
Oren Z. Kraus, Lei Jimmy Ba, Brendan J. Frey
Classifying and segmenting microscopy images with deep multiple instance learning. Bioinform. 32 (12) (2016)
Jimmy Ba, Roger B. Grosse, Ruslan Salakhutdinov, Brendan J. Frey
Learning Wake-Sleep Recurrent Attention Models. CoRR (2015)
Jimmy Ba, Ruslan Salakhutdinov, Roger B. Grosse, Brendan J. Frey
Learning Wake-Sleep Recurrent Attention Models. NIPS (2015)
Oren Z. Kraus, Lei Jimmy Ba, Brendan J. Frey
Classifying and Segmenting Microscopy Images Using Convolutional Multiple Instance Learning. CoRR (2015)
Alireza Makhzani, Brendan J. Frey
Winner-Take-All Autoencoders. NIPS (2015)
Siamak Ravanbakhsh, Christopher Srinivasa, Brendan J. Frey, Russell Greiner
Min-Max Problems on Factor Graphs. ICML (2014)
Alireza Makhzani, Brendan J. Frey
A Winner-Take-All Method for Training Sparse Convolutional Autoencoders. CoRR (2014)
Alireza Makhzani, Brendan J. Frey
k-Sparse Autoencoders. ICLR (Poster) (2014)
Michael K. K. Leung, Hui Yuan Xiong, Leo J. Lee, Brendan J. Frey
Deep learning of the tissue-regulated splicing code. Bioinform. 30 (12) (2014)
Siamak Ravanbakhsh, Russell Greiner, Brendan J. Frey
Training Restricted Boltzmann Machine by Perturbation. CoRR (2014)
Vladimir Pavlovic, Brendan J. Frey, Thomas S. Huang
Variational Learning in Mixed-State Dynamic Graphical Models CoRR (2013)
Kannan Achan, Brendan J. Frey, Ralf Koetter
A Factorized Variational Technique for Phase Unwrapping in Markov Random Fields CoRR (2013)
Clement Chung, Andrew Emili, Brendan J. Frey
Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. Bioinform. 29 (7) (2013)
Lei Jimmy Ba, Brendan J. Frey
Adaptive dropout for training deep neural networks. NIPS (2013)
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, Leah H. Matzat, Ryan K. Dale, Sarah A. Smith, Christopher A. Yarosh, Seth M. Kelly, Behnam Nabet, Desirea Mecenas, Weimin Li, Rakesh S. Laishram, Mei Qiao, Howard D. Lipshitz, Fabio Piano, Anita H. Corbett, Russ P. Carstens, Brendan J. Frey, Richard A. Anderson, Kristen W. Lynch, Luiz O. F. Penalva, Elissa P. Lei, Andrew G. Fraser, Benjamin J. Blencowe, Quaid Morris, Timothy R. Hughes
A compendium of RNA-binding motifs for decoding gene regulation. Nat. 499 (7457) (2013)
Brendan J. Frey, Nebojsa Jojic
Learning Graphical Models of Images, Videos and Their Spatial Transformations CoRR (2013)
Inmar E. Givoni, Clement Chung, Brendan J. Frey
Hierarchical Affinity Propagation CoRR (2012)
Jim C. Huang, Brendan J. Frey
Cumulative distribution networks and the derivative-sum-product algorithm CoRR (2012)
Patrick S. Li, Brendan J. Frey
Factorizing appearance using epitomic flobject analysis. CVPR (2012)
Boyko Kakaradov, Hui Yuan Xiong, Leo J. Lee, Nebojsa Jojic, Brendan J. Frey
Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data. BMC Bioinform. 13 (S-6) (2012)
Yongyi Mao, Frank R. Kschischang, Brendan J. Frey
Convolutional Factor Graphs as Probabilistic Models CoRR (2012)
Rómer Rosales, Brendan J. Frey
Learning Generative Models of Similarity Matrices CoRR (2012)
Daniel Tarlow, Richard S. Zemel, Brendan J. Frey
Flexible Priors for Exemplar-based Clustering CoRR (2012)
Jeroen Chua, Inmar E. Givoni, Ryan Prescott Adams, Brendan J. Frey
Learning structural element patch models with hierarchical palettes. CVPR (2012)
Daniel Tarlow, Kevin Swersky, Richard S. Zemel, Ryan Prescott Adams, Brendan J. Frey
Fast Exact Inference for Recursive Cardinality Models CoRR (2012)
Inmar E. Givoni, Vincent Cheung, Brendan J. Frey
Matrix Tile Analysis. CoRR (2012)
Daniel Tarlow, Kevin Swersky, Richard S. Zemel, Ryan Prescott Adams, Brendan J. Frey
Fast Exact Inference for Recursive Cardinality Models. UAI (2012)
Kevin Swersky, Daniel Tarlow, Ryan P. Adams, Richard S. Zemel, Brendan J. Frey
Probabilistic n-Choose-k Models for Classification and Ranking. NIPS (2012)
Brendan J. Frey
Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models CoRR (2012)
Hui Yuan Xiong, Yoseph Barash, Brendan J. Frey
Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context. Bioinform. 27 (18) (2011)
Inmar E. Givoni, Clement Chung, Brendan J. Frey
Hierarchical Affinity Propagation. UAI (2011)
Clement Chung, Jian Liu, Andrew Emili, Brendan J. Frey
Computational refinement of post-translational modifications predicted from tandem mass spectrometry. Bioinform. 27 (6) (2011)
Daniel Tarlow, Inmar E. Givoni, Richard S. Zemel, Brendan J. Frey
Interpreting Graph Cuts as a Max-Product Algorithm CoRR (2011)
Patrick S. Li, Inmar E. Givoni, Brendan J. Frey
Learning better image representations using 'flobject analysis'. CVPR (2011)
Daniel Tarlow, Inmar E. Givoni, Richard S. Zemel, Brendan J. Frey
Graph Cuts is a Max-Product Algorithm. UAI (2011)
Jim C. Huang, Brendan J. Frey
Cumulative Distribution Networks and the Derivative-sum-product Algorithm: Models and Inference for Cumulative Distribution Functions on Graphs. J. Mach. Learn. Res. 12 (2011)
Yoseph Barash, Benjamin J. Blencowe, Brendan J. Frey
Model-based detection of alternative splicing signals. Bioinform. 26 (12) (2010)
Yoseph Barash, John A. Calarco, Weijun Gao, Qun Pan, Xinchen Wang, Ofer Shai, Benjamin J. Blencowe, Brendan J. Frey
Deciphering the splicing code. Nat. 465 (7294) (2010)
Nevena Lazic, Brendan J. Frey, Parham Aarabi
Solving the Uncapacitated Facility Location Problem Using Message Passing Algorithms. AISTATS (2010)
Nebojsa Jojic, Alessandro Perina, Marco Cristani, Vittorio Murino, Brendan J. Frey
Stel component analysis: Modeling spatial correlations in image class structure. CVPR (2009)
Nevena Lazic, Inmar E. Givoni, Brendan J. Frey, Parham Aarabi
FLoSS: Facility location for subspace segmentation. ICCV (2009)
Stark C. Draper, Frank R. Kschischang, Brendan J. Frey
Rateless coding for arbitrary channel mixtures with decoder channel state information. IEEE Trans. Inf. Theory 55 (9) (2009)
Inmar E. Givoni, Brendan J. Frey
Semi-Supervised Affinity Propagation with Instance-Level Constraints. AISTATS (2009)
Inmar E. Givoni, Brendan J. Frey
A Binary Variable Model for Affinity Propagation. Neural Comput. 21 (6) (2009)
Jim C. Huang, Brendan J. Frey
Cumulative distribution networks and the derivative-sum-product algorithm. UAI (2008)
Anitha Kannan, Nebojsa Jojic, Brendan J. Frey
Fast Transformation-Invariant Component Analysis. Int. J. Comput. Vis. 77 (1-3) (2008)
Vincent Cheung, Brendan J. Frey, Nebojsa Jojic
Video Epitomes. Int. J. Comput. Vis. 76 (2) (2008)
Daniel Tarlow, Richard S. Zemel, Brendan J. Frey
Flexible Priors for Exemplar-based Clustering. UAI (2008)
Jim C. Huang, Brendan J. Frey, Quaid Morris
Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3. Pacific Symposium on Biocomputing (2008)
Delbert Dueck, Brendan J. Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili, Gabe Musso, Robert Hegele
Constructing Treatment Portfolios Using Affinity Propagation. RECOMB (2008)
Jim C. Huang, Brendan J. Frey
Structured ranking learning using cumulative distribution networks. NIPS (2008)
Delbert Dueck, Brendan J. Frey
Non-metric affinity propagation for unsupervised image categorization. ICCV (2007)
Brendan J. Frey
Learning in Biomedicine and Bioinformatics Using Affinity Propagation. ICMLA (2007)
Anitha Kannan, Andrew Emili, Brendan J. Frey
A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements. RECOMB (2007)
Jim C. Huang, Quaid Morris, Brendan J. Frey
Bayesian Inference of MicroRNA Targets from Sequence and Expression Data. J. Comput. Biol. 14 (5) (2007)
Steven J. Rennie, Parham Aarabi, Brendan J. Frey
Variational Probabilistic Speech Separation Using Microphone Arrays. IEEE Trans. Speech Audio Process. 15 (1) (2007)
Brendan J. Frey, Quaid Morris, Timothy R. Hughes
GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data. J. Comput. Biol. 13 (2) (2006)
Inmar E. Givoni, Vincent Cheung, Brendan J. Frey
Matrix Tile Analysis. UAI (2006)
Lei Ying, Zhi-Pei Liang, David C. Munson, Ralf Koetter, Brendan J. Frey
Unwrapping of MR phase images using a Markov random field model. IEEE Trans. Medical Imaging 25 (1) (2006)
Ofer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey
Inferring global levels of alternative splicing isoforms using a generative model of microarray data. Bioinform. 22 (5) (2006)
Jim C. Huang, Quaid Morris, Brendan J. Frey
Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data. RECOMB (2006)
Brendan J. Frey
Beyond genomics: Detecting codes and signals in the cellular transcriptome [Plenary speakers]. ISIT (2006)
Brendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes
GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data. Pacific Symposium on Biocomputing (2005)
Brendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes
Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model. RECOMB (2005)
Anitha Kannan, Nebojsa Jojic, Brendan J. Frey
Generative Model for Layers of Appearance and Deformation. AISTATS (2005)
Jim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey
GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data. ISMB (Supplement of Bioinformatics) (2005)
Brendan J. Frey, Delbert Dueck
Mixture Modeling by Affinity Propagation. NIPS (2005)
Kannan Achan, Sam T. Roweis, Aaron Hertzmann, Brendan J. Frey
A segment based probabilistic generative model of speech. ICASSP (5) (2005)
Vincent Cheung, Brendan J. Frey, Nebojsa Jojic
Video Epitomes. CVPR (1) (2005)
Steven J. Rennie, Kannan Achan, Brendan J. Frey, Parham Aarabi
Variational Speech Separation of More Sources than Mixtures. AISTATS (2005)
Nebojsa Jojic, Vladimir Jojic, Brendan J. Frey, Christopher Meek, David Heckerman
Using epitomes to model genetic diversity: Rational design of HIV vaccines. NIPS (2005)
Delbert Dueck, Quaid Morris, Brendan J. Frey
Multi-way clustering of microarray data using probabilistic sparse matrix factorization. ISMB (Supplement of Bioinformatics) (2005)
Brendan J. Frey, Nebojsa Jojic
A Comparison of Algorithms for Inference and Learning in Probabilistic Graphical Models. IEEE Trans. Pattern Anal. Mach. Intell. 27 (9) (2005)
Anitha Kannan, Brendan J. Frey, Nebojsa Jojic
A Generative Model of Dense Optical Flow in Layers. SCVMA (2004)
Rómer Rosales, Kannan Achan, Brendan J. Frey
Learning to cluster using local neighborhood structure. ICML (2004)
Ofer Shai, Brendan J. Frey, Quaid Morris, Qun Pan, Christine Misquitta, Benjamin J. Blencowe
Probabilistic Inference of Alternative Splicing Events in Microarray Data. NIPS (2004)
Yongyi Mao, Frank R. Kschischang, Brendan J. Frey
Convolutional Factor Graphs as Probabilistic Models. UAI (2004)
Stark C. Draper, Brendan J. Frey, Frank R. Kschischang
On interacting encoders and decoders in multiuser settings. ISIT (2004)
Stark C. Draper, Brendan J. Frey, Frank R. Kschischang
Efficient variable length channel coding for unknown DMCs. ISIT (2004)
Nemanja Petrovic, Nebojsa Jojic, Brendan J. Frey, Thomas S. Huang
Real-time On-line Learning of Transformed Hidden Markov Models from Video. AISTATS (2003)
Brendan J. Frey
Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models. UAI (2003)
Quaid Morris, Brendan J. Frey
Denoising and Untangling Graphs Using Degree Priors. NIPS (2003)
Brendan J. Frey, Nebojsa Jojic, Anitha Kannan
Learning Appearance and Transparency Manifolds of Occluded Objects in Layers. CVPR (1) (2003)
Steven J. Rennie, Parham Aarabi, Trausti T. Kristjansson, Brendan J. Frey, Kannan Achan
Robust variational speech separation using fewer microphones than speakers. ICASSP (1) (2003)
Rómer Rosales, Kannan Achan, Brendan J. Frey
Unsupervised Image Translation. ICCV (2003)
Nebojsa Jojic, Brendan J. Frey, Anitha Kannan
Epitomic analysis of appearance and shape. ICCV (2003)
Rómer Rosales, Brendan J. Frey
Learning Generative Models of Similarity Matrices. UAI (2003)
Kannan Achan, Sam T. Roweis, Brendan J. Frey
Probabilistic Inference of Speech Signals from Phaseless Spectrograms. NIPS (2003)
Brendan J. Frey, Nebojsa Jojic
Transformation-Invariant Clustering Using the EM Algorithm. IEEE Trans. Pattern Anal. Mach. Intell. 25 (1) (2003)

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Publication Activity (10 Years)

Top Topics

Top Venues

Brendan J. Frey