Brendan J. Frey - researchr alias

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Viewing Publication 1 - 100 from 136

2018

COSSMO: predicting competitive alternative splice site selection using deep learningHannes Bretschneider, Shreshth Gandhi, Amit G. Deshwar, Khalid Zuberi, Brendan J. Frey. bioinformatics, 34(13), 2018. [doi]

Inference of the human polyadenylation codeMichael K. K. Leung, Andrew Delong, Brendan J. Frey. bioinformatics, 34(17):2889-2898, 2018. [doi]

2017

Inference of the Human Polyadenylation CodeMichael K. K. Leung, Andrew Delong, Brendan J. Frey. recomb 2017: 379 [doi]

PixelGAN AutoencodersAlireza Makhzani, Brendan J. Frey. nips 2017: 1972-1982 [doi]

Min-Max PropagationChristopher Srinivasa, Inmar E. Givoni, Siamak Ravanbakhsh, Brendan J. Frey. nips 2017: 5571-5579 [doi]

2016

2015

Learning Wake-Sleep Recurrent Attention ModelsJimmy Ba, Ruslan Salakhutdinov, Roger B. Grosse, Brendan J. Frey. nips 2015: 2593-2601 [doi]

Winner-Take-All AutoencodersAlireza Makhzani, Brendan J. Frey. nips 2015: 2791-2799 [doi]

2014

Deep learning of the tissue-regulated splicing codeMichael K. K. Leung, Hui Yuan Xiong, Leo J. Lee, Brendan J. Frey. bioinformatics, 30(12):121-129, 2014. [doi]

2013

Bayesian Painting by Numbers: Flexible Priors for Colour-Invariant Object RecognitionJeroen C. Chua, Inmar E. Givoni, Ryan P. Adams, Brendan J. Frey. In Roberto Cipolla, Sebastiano Battiato, Giovanni Maria Farinella, editors, Machine Learning for Computer Vision. Volume 411 of Studies in Computational Intelligence, pages 89-117, Springer, 2013. [doi]

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometryClement Chung, Andrew Emili, Brendan J. Frey. bioinformatics, 29(7):821-829, 2013. [doi]

2012

2011

Computational refinement of post-translational modifications predicted from tandem mass spectrometryClement Chung, Jian Liu, Andrew Emili, Brendan J. Frey. bioinformatics, 27(6):797-806, 2011. [doi]

Hierarchical Affinity PropagationInmar E. Givoni, Clement Chung, Brendan J. Frey. uai 2011: 238-246 [doi]

STORMSeq: A Method for Ranking Regulatory Sequences by Integrating Experimental Datasets with Diverse Computational PredictionsJim C. Huang, Brendan J. Frey. In Henry Horng-Shing Lu, Bernhard Schölkopf, Hongyu Zhao, editors, Handbook of Statistical Bioinformatics. Springer Handbooks of Computational Statistics, pages 109-134, Springer, 2011. [doi]

Cumulative Distribution Networks and the Derivative-sum-product Algorithm: Models and Inference for Cumulative Distribution Functions on GraphsJim C. Huang, Brendan J. Frey. jmlr, 12:301-348, 2011. [doi]

Learning better image representations using flobject analysis Patrick S. Li, Inmar E. Givoni, Brendan J. Frey. cvpr 2011: 2721-2728 [doi]

Graph Cuts is a Max-Product AlgorithmDaniel Tarlow, Inmar E. Givoni, Richard S. Zemel, Brendan J. Frey. uai 2011: 671-680 [doi]

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular contextHui Yuan Xiong, Yoseph Barash, Brendan J. Frey. bioinformatics, 27(18):2554-2562, 2011. [doi]

2010

2009

2008

Video EpitomesVincent Cheung, Brendan J. Frey, Nebojsa Jojic. ijcv, 76(2):141-152, 2008. [doi]

Constructing Treatment Portfolios Using Affinity PropagationDelbert Dueck, Brendan J. Frey, Nebojsa Jojic, Vladimir Jojic, Guri Giaever, Andrew Emili, Gabe Musso, Robert Hegele. recomb 2008: 360-371 [doi]

Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3Jim C. Huang, Brendan J. Frey, Quaid Morris. psb 2008: 52-63 [doi]

Structured ranking learning using cumulative distribution networksJim C. Huang, Brendan J. Frey. nips 2009: 697-704 [doi]

Cumulative distribution networks and the derivative-sum-product algorithmJim C. Huang, Brendan J. Frey. uai 2008: 290-297 [doi]

Fast Transformation-Invariant Component AnalysisAnitha Kannan, Nebojsa Jojic, Brendan J. Frey. ijcv, 77(1-3):87-101, 2008. [doi]

Flexible Priors for Exemplar-based ClusteringDaniel Tarlow, Richard S. Zemel, Brendan J. Frey. uai 2008: 537-545 [doi]

2007

2006

Beyond genomics: Detecting codes and signals in the cellular transcriptome [Plenary speakers]Brendan J. Frey. isit 2006: [doi]

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray DataBrendan J. Frey, Quaid Morris, Timothy R. Hughes. jcb, 13(2):200-214, 2006. [doi]

Matrix Tile AnalysisInmar Givoni, Vincent Cheung, Brendan J. Frey. uai 2006: [doi]

Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression DataJim C. Huang, Quaid Morris, Brendan J. Frey. recomb 2006: 114-129 [doi]

Inferring global levels of alternative splicing isoforms using a generative model of microarray dataOfer Shai, Quaid Morris, Benjamin J. Blencowe, Brendan J. Frey. bioinformatics, 22(5):606-613, 2006. [doi]

Unwrapping of MR phase images using a Markov random field modelLei Ying, Zhi-Pei Liang, David C. Munson, Ralf Koetter, Brendan J. Frey. tmi, 25(1):128-136, 2006. [doi]

2005

A segment based probabilistic generative model of speechKannan Achan, Sam T. Roweis, Aaron Hertzmann, Brendan J. Frey. icassp 2005: 221-224 [doi]

Video EpitomesVincent Cheung, Brendan J. Frey, Nebojsa Jojic. cvpr 2005: 42-49 [doi]

Multi-way clustering of microarray data using probabilistic sparse matrix factorizationDelbert Dueck, Quaid Morris, Brendan J. Frey. ismb 2005: 144-151 [doi]

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate ModelBrendan J. Frey, Quaid Morris, Mark D. Robinson, Timothy R. Hughes. recomb 2005: 66-82 [doi]

Mixture Modeling by Affinity PropagationBrendan J. Frey, Delbert Dueck. nips 2005: 379-386 [doi]

GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray DataBrendan J. Frey, Quaid Morris, Wen Zhang, Naveed Mohammad, Timothy R. Hughes. psb 2005: [doi]

A Comparison of Algorithms for Inference and Learning in Probabilistic Graphical ModelsBrendan J. Frey, Nebojsa Jojic. pami, 27(9):1392-1416, 2005. [doi]

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray dataJim C. Huang, Quaid Morris, Timothy R. Hughes, Brendan J. Frey. ismb 2005: 222-231 [doi]

Using epitomes to model genetic diversity: Rational design of HIV vaccinesNebojsa Jojic, Vladimir Jojic, Brendan J. Frey, Christopher Meek, David Heckerman. nips 2005: 587-594 [doi]

Generative Model for Layers of Appearance and DeformationAnitha Kannan, Nebojsa Jojic, Brendan J. Frey. aistats 2005: 166-173 [doi]

Variational Speech Separation of More Sources than MixturesSteven J. Rennie, Kannan Achan, Brendan J. Frey, Parham Aarabi. aistats 2005: 293-300 [doi]

2004

2003

Probabilistic Inference of Speech Signals from Phaseless SpectrogramsKannan Achan, Sam T. Roweis, Brendan J. Frey. nips 2004: 1393-1400 [doi]

Extending Factor Graphs so as to Unify Directed and Undirected Graphical ModelsBrendan J. Frey. uai 2003: 257-264

Learning Appearance and Transparency Manifolds of Occluded Objects in LayersBrendan J. Frey, Nebojsa Jojic, Anitha Kannan. cvpr 2003: 45-52 [doi]

Transformation-Invariant Clustering Using the EM AlgorithmBrendan J. Frey, Nebojsa Jojic. pami, 25(1):1-17, 2003. [doi]

Epitomic analysis of appearance and shapeNebojsa Jojic, Brendan J. Frey, Anitha Kannan. iccv 2003: 34-43 [doi]

Denoising and Untangling Graphs Using Degree PriorsQuaid Morris, Brendan J. Frey. nips 2004: 385-392 [doi]

Real-time On-line Learning of Transformed Hidden Markov Models from VideoNemanja Petrovic, Nebojsa Jojic, Brendan J. Frey, Thomas S. Huang. aistats 2003: 225-232 [doi]

Robust variational speech separation using fewer microphones than speakersSteven J. Rennie, Parham Aarabi, Trausti T. Kristjansson, Brendan J. Frey, Kannan Achan. icassp 2003: 88-91 [doi]

Robust variational speech separation using fewer microphones than speakersSteven J. Rennie, Parham Aarabi, Trausti T. Kristjansson, Brendan J. Frey, Kannan Achan. icmcs 2004: 741-744 [doi]

Learning Generative Models of Similarity MatricesRómer Rosales, Brendan J. Frey. uai 2003: 485-492

Unsupervised Image TranslationRómer Rosales, Kannan Achan, Brendan J. Frey. iccv 2003: 472-478 [doi]

Multibaseline InSAR terrain elevation estimation: a dynamic programming approachLei Ying, David C. Munson, Ralf Koetter, Brendan J. Frey. icip 2003: 157-160

2002

Phase unwrapping by minimizing Kikuchi free energyKannan Achan, Brendan J. Frey, Ralf Koetter, David C. Munson. igarss 2002: 1738-1740 [doi]

Fast Transformation-Invariant Factor AnalysisAnitha Kannan, Nebojsa Jojic, Brendan J. Frey. nips 2003: 1263-1270 [doi]

Accounting for uncertainity in observations: A new paradigm for Robust Automatic Speech RecognitionTrausti T. Kristjansson, Brendan J. Frey. icassp 2002: 61-64 [doi]

Noise robust speech recognition using Gaussian basis functions for non-linear likelihood function approximationChris Pal, Brendan J. Frey, Trausti T. Kristjansson. icassp 2002: 405-408 [doi]

Learning Montages of Transformed Latent Images as Representations of Objects That Change in AppearanceChris Pal, Brendan J. Frey, Nebojsa Jojic. eccv 2002: 715-731 [doi]

Balancing rewrapping error and smoothness in two dimensional phase unwrapping problemsDavid C. Schultz, Ralf Koetter, Brendan J. Frey, David C. Munson Jr.. igarss 2002: 2507-2509 [doi]

Combination of statistical and rule-based approaches for spoken language understandingYe-Yi Wang, Alex Acero, Ciprian Chelba, Brendan J. Frey, Leon Wong. interspeech 2002: 609-612 [doi]

An iterative dynamic programming approach to 2-D phase unwrappingLei Ying, Brendan J. Frey, Ralf Koetter, David C. Munson. igarss 2002: 469-471 [doi]

An iterative dynamic programming approach to 2-D phase unwrappingLei Ying, David C. Munson, Ralf Koetter, Brendan J. Frey. icip 2002: 469-471

2001

Very loopy belief propagation for unwrapping phase imagesBrendan J. Frey, Ralf Koetter, Nemanja Petrovic. nips 2001: 737-743 [doi]

"Codes" on images and iterative phase unwrappingBrendan J. Frey, Ralf Koetter, Nemanja Petrovic. itw 2001: 9-11 [doi]

Signal-space characterization of iterative decodingBrendan J. Frey, Ralf Koetter, Alexander Vardy. TIT, 47(2):766-781, 2001.

ALGONQUIN - Learning Dynamic Noise Models From Noisy Speech for Robust Speech RecognitionBrendan J. Frey, Trausti T. Kristjansson, Li Deng, Alex Acero. nips 2001: 1165-1171 [doi]

ALGONQUIN: iterating laplace s method to remove multiple types of acoustic distortion for robust speech recognitionBrendan J. Frey, Li Deng, Alex Acero, Trausti T. Kristjansson. interspeech 2001: 901-904 [doi]

Unwrapping phase images by propagating probabilities across graphsRalf Koetter, Brendan J. Frey, Nemanja Petrovic, David C. Munson Jr.. icassp 2001: 1845-1848 [doi]

Towards non-stationary model-based noise adaptation for large vocabulary speech recognitionTrausti T. Kristjansson, Brendan J. Frey, Li Deng, Alex Acero. icassp 2001: 337-340 [doi]

Factor graphs and the sum-product algorithmFrank R. Kschischang, Brendan J. Frey, Hans-Andrea Loeliger. TIT, 47(2):498-519, 2001.

Enforcing Integrability for Surface Reconstruction Algorithms Using Belief Propagation in Graphical ModelsNemanja Petrovic, Ira Cohen, Brendan J. Frey, Ralf Koetter, Thomas S. Huang. cvpr 2001: 743-748 [doi]

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