Structured ranking learning using cumulative distribution networks (pdf)
J.C. Huang and B.J. Frey
Advances in Neural Information Processing Systems 21, January 2009.
Semi-Supervised Affinity Propagation with
Instance-Level Constraints (pdf)
Inmar E. Givoni, Brendan J. Frey
Proceedings of the 12th International Conference on Arti cial Intelligence and Statistics (AISTATS), April 2009.
Affinity Propagation: Clustering Data by Passing Messages (pdf)
Dueck, Delbert
University of Toronto Ph.D. thesis, June 2009.
Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes (jrnl) (PubMed)
Benjamin J. Blencowe, Sidrah Ahmad and Leo J. Lee
Genes & Development, 23(12): 1379-1386, June 2009.
A Binary Variable Model for Affinity Propagation (pdf) (jrnl) (PubMed)
Inmar E. Givoni, Brendan J. Frey
Neural Computation, Vol. 21, No. 6, Pages 1589-1600, June 2009.
FLoSS: Facility Location for Subspace Segmentation (pdf)
Nevena Lazic, Inmar Givoni, Brendan Frey, Parham Aarabi
Proceedings of the 12th IEEE International Conference on Computer Vision (ICCV), September 2009.
Comparing sequence and expression for predicting microRNA targets using GenMiR3 (pdf)
J.C. Huang, B.J. Frey and Q.D. Morris
Pacific Symposium for Biocomputing (PSB) 13: 52-63, January 2008.
AFFINITY PROPAGATION and the VERTEX SUBSTITUTION HEURISTIC (jrnl)
Brendan J. Frey, Delbert Dueck
January 2008.
Flexible priors for exemplar-based clustering (pdf)
D. Tarlow, R. Zemel, B. J. Frey
Proceedings of the 24th Conference on Uncertainty in Artificial Intelligence, January 2008.
Morgan Kaufmann, San Francisco, CA, 7 pages.
Constructing Treatment Portfolios Using Affinity Propagation (pdf)
Dueck, D., Frey, B.J., Jojic, N. and Jojic, V.
International Conference on Research in Computational Molecular Biology (RECOMB), Singapore (presented 01/04/2008)., January 2008.
Constructing Treatment Portfolios using Affinity Propagation (pdf) (jrnl)
D. Dueck, B.J. Frey, N. Jojic, V. Jojic, G. Giaever, A. Emili, G. Musso and R. Hegele
Research in Computational Molecular Biology (RECOMB), April 2008.
A systematic analysis of intronic sequences downstream of 5\' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation (jrnl) (PubMed)
I Aznarez, Y Barash, O Shai, D He, J Zielenski, LC Tsui, J Parkinson, B Frey, JM Rommens, B Blencowe
Genome Research, doi: 10.1101/gr.073155.107, May 2008.
Fast transformation-invariant component analysis (pdf)
A. Kannan, N. Jojic, B. J. Frey
International Journal of Computer Vision 77:1, 87-101, May 2008.
Primary Author.
Cumulative distribution networks and the derivative-sum-product algorithm (pdf)
J. C. Huang and B. J. Frey
Proceedings of the Twenty-Fourth Conference on Uncertainty in Artificial Intelligence (UAI), July 2008.
(Best Student Paper Runner-up)..
Inferring Alternative Splicing Combinations from Comprehensive Putative-Junction Microarray Data (pdf)
Leo J. Lee, Brendan J. Frey, Qun Pan, Christine Misquitta, and Benjamin J. Blencowe
University of Toronto Technical Report PSI-2008-01, October 2008.
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing (PubMed)
Pan, Q., Shai, O., Lee, L.J., Frey, B.J., and Blencowe, B.J.
Nat. Genet. 40(12):1413-1415, November 2008.
Structured ranking learning using cumulative distribution networks (pdf)
J. C. Huang, B. J. Frey
Neural Information Processing Systems Conference 21, December 2008.
(MIT Press, Cambridge, MA, 2009, 7 pages).
Variational probabilistic speech separation using microphone arrays (pdf)
S. Rennie, P. Aarabi, B. J. Frey
IEEE Transactions on Audio, Speech and Language Processing 15:1, 135-149, January 2007.
Primary Author.
A Bayesian model that links microarray mRNA measurements to mass spectrometry protein measurements (pdf)
A. Kannan, A. Emili, B. J. Frey
Proceedings Eleventh International Conference on Research in Computational Molecular Biology, 325-338, January 2007.
Nonmetric affinity propagation for unsupervised image categorization (pdf)
D. Dueck, B. J. Frey
Proceedings IEEE International Conference on Computer Vision, January 2007.
IEEE Computer Society Press, Los Alamitos, CA, 8 pages.
Clustering by passing messages between data points (pdf) (Perspective by Marc Mezard)
Brendan J. Frey and Delbert Dueck
Science, Vol 315, No 5814, pp 972-976, February 2007.
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes (pdf)
B. Cox, T. Kislinger, D.A. Wigle, A. Kannan, K. Brown, T. Okubo , B. Hogan, I. Jurisica, B.J. Frey, J. Rossant, A. Emili
Molecular Systems Biology 3:109, May 2007.
Capturing Long-Range Correlations with Patch Models (pdf)
V. Cheung, N. Jojic, and D. Samaras
In Proc. IEEE Intern. Conf. Computer Vision and Pattern Recognition (CVPR), June 2007.
Bayesian inference of microRNA targets from sequence and expression data. (pdf)
J.C. Huang, Q.D. Morris and B.J. Frey
J. Comp. Bio. 14(5): 550-563., June 2007.
Functional coordination of alternative splicing in the mammalian central nervous system (pdf)
M. Fagnani*, Y. Barash*, J. Y. Ip, C. Misquitta, Q. Pan, A. Saltzman, O Shai, L. Lee, A. Rozenhek, N. Mohammad, S. Willaime-Morawek, T. Babak, W. Zhang, T. R. Hughes, D. Kooy, B. J. Frey and B. J. Blencowe
Genome Biology 2007, 8:R108, June 2007.
(*): joint first authors.
Functional coordination of alternative splicing in the mammalian central nervous system (pdf)
M. Fagnani, Y. Barash, J. Y. Ip, C. Misquitta, Q. Pan, A. Saltzman, O. Shai, L. Lee, A. Rozenhek, N. Mohammad, S. Willaime-Morawek, T. Babak, W. Zhang, T. R. Hughes, D. Kooy, B. J. Frey and B. J. Blencowe
Genome Biology 8, June 2007.
Primary Author.
Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations (pdf)
J.C. Huang, A. Kannan and J. Winn
Bioinformatics 23:i212-221, July 2007.
Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & Sixth European Conference on Computational Biology (ECCB).
Comparing sequence and expression for predicting microRNA targets using GenMiR3 (pdf)
J. C. Huang, B.J. Frey, Q.D. Morris
Proceedings Pacific Symposium for Biocomputing (PSB) 13, 52-63, September 2007.
Non-metric affinity propagation for unsupervised image categorization (pdf)
Dueck, D. and Frey, B.J.
Proceedings of the IEEE International Conference on Computer Vision (ICCV), October 2007.
Using expression profiling data to identify human microRNA targets (pdf)
J.C. Huang*, T. Babak*, T.W. Corson, G. Chua, S. Khan, B.L. Gallie, T.R. Hughes, B.J. Blencowe, B.J. Frey and Q.D. Morris
Nature Methods, Vol. 4, No. 12, November 2007.
(*): joint first authors.
Using expression profiling data to identify human microRNA targets (pdf)
J. C. Huang, T. Babak, T. W. Corson, G. Chua, S. Khan, B. L. Gallie, T. R. Hughes, B. J. Frey, Q. D. Morris
Nature Methods 4:12, 1049-1055, November 2007.
Inferring global levels of alternative splicing isoforms using a generative model of microarray data (pdf) (jrnl)
O. Shai, Q. D. Morris, B. J. Blencowe, and B. J. Frey
Bioinformatics 22(5):606-613, January 2006.
Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression (PubMed)
Q. Pan, A.L. Saltzman, Y.K. Kim, C. Misquitta, O. Shai, L.E. Maquat, B.J. Frey, and B.J. Blencowe
Genes and Development, 20(2):153-8, January 2006.
Mixture modeling by Affinity Propagation (pdf)
Frey, B.J. and Dueck, D.
Neural Information Processing Systems 18: 379-386, January 2006.
Unwrapping of MR phase images using a Markov random field model (pdf)
L. Ying, Z.-P. Liang, D. C. Munson, Jr., R. Koetter and B. J. Frey
IEEE Transactions on Medical Imaging 25, 128-136, January 2006.
Using epitomes to model genetic diversity: Rational design of HIV vaccines (pdf)
N. Jojic, V. Jojic, B. J. Frey, C. Meek, D. Heckerman
Neural Information Processing Systems Conference 18, Dec, 2005, January 2006.
(MIT Press, Cambridge, MA, 2006, 7 pages).
Mixture modeling by affinity propagation (pdf)
B. J. Frey, D. Dueck
Neural Information Processing Systems Conference 18, Dec, 2005, January 2006.
(MIT Press, Cambridge, MA, 2006, 7 pages).
How Many New Genes Are There? (pdf) (jrnl) (PubMed)
Leo J. Lee, Timothy R. Hughes, and Brendan J. Frey
Science, Vol. 311, No. 5768, pp. 1709, March 2006.
Inferring global levels of alternative splicing isoforms using a generative model of microarray data (pdf)
O. Shai, Q. D. Morris, B. J. Blencowe and B. J. Frey
Bioinformatics 22:5, 606-613, March 2006.
Detecting microRNA targets by linking sequence, microRNA and gene expression data
J.C. Huang, Q.D. Morris and B.J. Frey
Lecture Notes in Computer Science, Springer-Verlag, 3909: 114-129, April 2006.
Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB).
Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling (pdf)
Thomas Kislinger, Brian Cox, Anitha Kannan, Clement Chung, Pingzhao Hu, Alexandr Ignatchenko, Michelle S. Scott, Anthony O. Gramolini, Quaid Morris, Michael T. Hallett, Janet Rossant, Timothy R. Hughes, Brendan Frey, and Andrew Emili
Cell 125, 173–186, April 2006.
Factorgrams: A tool for visualizing multi-way associations in biological data (pdf)
V. Cheung, I. Givoni, D. Dueck, B. J. Frey
University of Toronto Technical Report PSI-2006-44, May 2006.
Matrix Tile Analysis (pdf)
Inmar Givoni, Vincent Cheung, and Brendan J. Frey
Presented at the 22nd Conference on Uncertainty in Artificial Intelligence (UAI), Cambridge, MA., July 2006.
Identifying transcription factor functions and targets by phenotypic activation (pdf)
G. Chua, Q. D. Morris, R. Sopko, M. D. Robinson, O. Ryan, E. T. Chan, B. J. Frey, B. Andrews, C. Boone, T. R. Hughes
Proc National Academy of Science 103:32, 12045-12050, July 2006.
Population Sequencing from Chromatogram Data (pdf)
Dueck, D., Abha, C., Moore, C., Sarich, J., Goodridge, D., Heckerman, D., Sayer, D., Mallal, S., Jojic, N.
International Conference on Intelligent Systems for Molecular Biology, July 2006.
PLoS oral track, presented 08/08/2006.
Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast (PubMed)
A.B. Parsons(*), A. Lopez(*), I.E. Givoni(*), D.E. Williams, C.A. Gray, J. Porter, G. Chua, R. Sopko, R.L. Brost, C. Ho, J.Wang, T. Ketela, C. Brenner, J.A. Brill, G.E. Fernandez , T.C. Lorenz , G.S. Payne, S. Ishihara, Y. Ohya, B. Andrews, T.R. Hughes, B.J. Frey, T.R. Graham, R.J. Andersen, C. Boone
Cell, Vol. 126, Issue 3, pp. 611-625, August 2006.
[(*): joint first authors].
Exploring the modeof- action of bioactive compounds by chemical-genetic profiling in yeast (pdf)
A. B. Parsons, A. Lopez, I. Givoni, D. Williams, G. Chua, R. Sopko, C. H. Ho, R. L. Brost, T. Ketela, B. Andrews, T. R. Hughes, B. J. Frey, T. R. Graham, R. Anderson, C. Boone
Cell 126:3, 611-625, August 2006.
Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression (pdf)
Q. Pan, A. L. Saltzman, Y. K. Kim, C. Misquitta, O. Shai, L. E. Maquat, B. J. Frey and B. J. Blencowe.
Genes & Development 20:2, January 2005.
A comparison of algorithms for inference and learning in probabilistic graphical models (pdf)
B. J. Frey and N. Jojic
IEEE Trans. Pattern Analysis and Machine Intelligence 27:9, 1392-1416, January 2005.
A generative model for layers of appearance and deformation (pdf)
A. Kannan, N. Jojic, B. J. Frey
Proc. Tenth International Workshop on Artificial Intelligence and Statistics, January 2005.
10 pages.
Variational speech separation of more sources than mixtures (pdf)
S. Rennie, K. Achan, P. Aarabi, B. J. Frey
Proc. Tenth International Workshop on Artificial Intelligence and Statistics, January 2005.
10 pages.
GenRate: A generative model that finds and scores new genes and exons in genomic microarray data (pdf)
B. J. Frey, Q. D. Morris,W. Zhang, N. Mohammad, T. R. Hughes
Proc. 2005 Pacific Symposium on Biocomputing, January 2005.
12 pages.
Probabilistic inference of alternative splicing events in microarray data (pdf)
O. Shai, B. J. Frey, Q. D. Morris, Q. Pan, C. Misquitta, B. J. Blencowe
Advances in Neural Information Processing Systems 17, January 2005.
MIT Press, Cambridge, MA, 7 pages.
Learning Rankings via Convex Hull Separation (pdf)
Glenn Fung, Rómer Rosales, and Balaji Krishnapuram
In Proc. Neural Information Processing Systems (NIPS) 2005, January 2005.
Focused Inference (pdf) (ps) (Slides)
Rómer Rosales and Tommi Jaakkola
In Artificial Intelligence and Statistics (AISTATS). Jan 2005, January 2005.
Multi-way clustering of microarray data using probabilistic sparse matrix factorization (pdf)
D. Dueck, Q. Morris, B. J. Frey
Proceedings of the 13th Annual International Conference on Intelligent Systems for Molecular Biology, June 2005, 144-151, March 2005.
Video epitomes (pdf)
V. Cheung, B. J. Frey, and N. Jojic
In Proc. IEEE Conf. Computer Vision and Pattern Recognition (CVPR), June 2005.
(Best paper honourable mention award).
GenXHC: A probabilistic generative model for cross-hybridization compensation in high-density, genome-wide microarray data (pdf)
J.C. Huang, Q.D. Morris, T.R. Hughes and B.J. Frey
Bioinformatics 21 Suppl 1:i222-i231, June 2005.
Thirteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB).
Probabilistic Sparse Matrix Factorization with an application to discovering gene functions in mouse mRNA expression data (pdf)
Dueck, D., Morris, Q., and Frey, B.J.
International Conference on Intelligent Systems for Molecular Biology (ISMB), June 2005.
GenXHC: A probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data (pdf)
J. Huang, Q. Morris, B. J. Frey
Proceedings of the 13th Annual International Conference on Intelligent Systems for Molecular Biology, 222-231, June 2005.
A computational high-throughput method for detecting microRNA targets (pdf)
J.C. Huang, Q.D. Morris and B.J. Frey
University of Toronto Technical Report PSI TR 2005-026, August 2005.
A comparison of algorithms for inference and learning in probabilistic graphical models (pdf)
Brendan J Frey and Nebojsa Jojis
IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol 27, No 9, pp 1-25, September 2005.
Genomewide analysis of mouse transcripts using exon microarrays and factor graphs (pdf)
B. J. Frey, N. Mohammad, Q. D. Morris, W. Zhang, M. D. Robinson, S. Mnaimneh, R. Chang, Q. Pan, N. Laurin, E. Sat, J. Rossant, B. G. Bruneau, J. Aubin, B. Blencowe, T. R. Hughes
Nature Genetics 37:9, 991-996, September 2005.
A segmental HMM for speech waveforms (pdf)
K. Achan, S. Roweis, A. Hertzmann, B. J. Frey
Proc. IEEE International Conference on Acoustics, Speech and Signal Processing, IEEE Operations Center, Piscataway, NJ, January 2004.
8 pages.
Denoising and untangling graphs using degree priors (pdf)
Q. Morris, B. J. Frey and C. J. Paige
Advances in Neural Information Processing Systems 16, January 2004.
MIT Press, Cambridge, MA, 7 pages.
Probabilistic inference of speech signals from phaseless spectrograms (pdf)
K. Achan, S. Roweis and B. J. Frey
Advances in Neural Information Processing Systems 16, January 2004.
MIT Press, Cambridge, MA, 7 pages.
Iterative analysis of microarray data (pdf)
D. Dueck, J. Huang, Q. D. Morris and B. J. Frey
Proceedings of the 44th Allerton Conference on Communication, Control and Computing, Champaign-Urbana, IL, January 2004.
Champaign-Urbana, IL.
Probabilistic Sparse Matrix Factorization (pdf)
Dueck, D. and Frey, B.J.
University of Toronto Technical Report PSI-2004-23, May 2004.
A generative model of dense optical flow in layers (pdf)
A. Kannan, B. J. Frey and N. Jojic
Proceedings of the Workshop on Spatial Coherence for Visual Motion Analysis, May 15, 2004, May 2004.
Prague, Czech Republic, 12 pages.
Learning to Cluster using Local Neighborhood Structure (pdf) (ps) (slides)
Rómer Rosales, Kannan Achan, and Brendan Frey
In Proc. International Conference on Machine Learning (ICML). Jul 2004., July 2004.
Probabilistic sparse matrix factorization (pdf)
D. Dueck, B. J. Frey
University of Toronto Technical Report PSI-2004-23, September 2004.
Iterated conditional modes for cross-hybridization compensation in DNA microarray data. (pdf)
J.C. Huang, Q.D. Morris, B.J. Frey
University of Toronto Technical Report PSI TR 2004-031, October 2004.
Probabilistic Inference of Alternative Splicing Events in Microarray Data (pdf) (ps)
O. Shai, B. J. Frey, Q. D. Morris, Q. Pan, C. Misquitta, and B. J. Blencowe
Advances in Neural Information Processing Systema (NIPS) 17, 2205, 1241-1248, December 2004.
The functional landscape of mouse gene expression (pdf) (jrnl) (PubMed)
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR
Journal of Biology 2004, 3:21, December 2004.
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform (pdf)
Q. Pan, O. Shai, C. Misquitta, W. Zhang, N. Mohammed, T. Babak, H. Siu, T. R. Hughes, Q. Morris, B. J. Frey, B. J. Blencowe
Molecular Cell 16, 929–941, December 2004.
The functional landscape of mouse gene expression (pdf)
W. Zhang, Q. D. Morris, R. Chang, O. Shai, M. A. Bakowski, N. Mitsakakis, N. Mohammad, M. Robinson, R. Zirnglibl, E. Somogyi,N. Laurin, W. T. Peng, N. Krogan, E. Eftekharpour, E. Sat, J. Grigull, Q. Pan, J. Greenblatt, M. Fehlings, D. van der Kooy, J. Aubin, B. G. Bruneau, J. Rossant, B. J. Blencowe, B. J. Frey, and T. R. Hughes
Journal of Biology 3:21, December 2004.
51 pages, incl supp info..
Epitomic analysis of appearance and shape (pdf)
N. Jojic, B. J. Frey and A. Kannan
Proceedings of the International Conference on Computer Vision, January 2003.
IEEE Comp. Soc. Press, Los Alamitos, CA, 9 pages.
Learning appearance and transparency manifolds of occluding objects in layers (pdf)
B. J. Frey and N. Jojic
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, January 2003.
IEEE Computer Society Press, Los Alamitos, CA, 9 pages.
Robust variational speech separation using fewer microphones than speakers (pdf)
S. Rennie, P. Aarabi, T. Kristjansson, B. J. Frey and K. Achan
Proc. IEEE International Conference on Acoustics, Speech and Signal Processing, January 2003.
IEEE Operations Center, Piscataway, NJ.
Fast transformation-invariant factor analysis (pdf)
A. Kannan, N. Jojic and B. J. Frey
Advances in Neural Information Processing Systems 15, January 2003.
MIT Press, Cambridge, MA, 7 pages.
Translating images by unsupervised estimation of switching filters (pdf)
R. Rosales, K. Achan, B. J. Frey
Proceedings of the IEEE Workshop on Statistical Signal Processing, January 2003.
A comparison of Kikuchi free energy, Bethe free energy, and Gibbs free energy using Monte Carlo simulations (pdf)
Dueck, D. and Frey, B.J.
University of Toronto Technical Report PSI-2003-20, January 2003.
A Framework for Heading-Guided Recognition of Human Activity (pdf)
Rómer Rosales and Stan Sclaroff
Computer Vision and Image Understanding Journal (CVIU) 2003. , January 2003.
A Panoramic View of Yeast Non-Coding RNA processing (pdf)
Wen-Tao Peng, Mark D. Robinson, Sanie Mnaimneh, Nevan J. Krogan, Gerard Cagney, Quaid Morris, Armaity P. Davierwala, Jörg Grigull, Xueqi Yang, Wen Zhang, Nicholas Mitsakakis, Owen W. Ryan, Nira Datta, Vladimir Jojic, Chris Pal, Veronica Canadien, Dawn Richards, Bryan Beattie, Lani F. Wu, Steven J. Altschuler, Sam Roweis, Andrew Emili, Brendan J. Frey, Jack F. Greenblatt, and Timothy R. Hughes
Cell, vol. 113, pp. 919-933, June 2003.
Learning Generative Models of Affinity Matrices (pdf)
Rómer Rosales and Brendan Frey
In Proc. 19th Conference on Uncertainty in Artificial Intelligence (UAI). Aug 2003., August 2003.
Translating Images by Unsupervised Estimation of Switching Filters (pdf)
Rómer Rosales, Kannan Achan, and Brendan Frey
In Proc. IEEE Workshop on Statistical Signal Processing (SSP) (invited paper). Sep 2003., September 2003.
Unsupervised image translation (pdf)
R. Rosales, K. Achan and B. J. Frey
Proceedings of the International Conference on Computer Vision, October 2003.
IEEE Comp. Soc. Press, Los Alamitos, CA, 9 pages.
Unsupervised Image Translation (pdf)
Rómer Rosales and Brendan Frey
In Proc. International Conference on Computer Vision (ICCV). Oct 2003., October 2003.
Learning Montages of Transformed Latent Images as Representations of Objects that Change in Appearance (pdf)
Pal, C., Frey, B. and Jojic, N.
the proceedings of ECCV: The European Conference on Computer Vision, Springer-Verlag lecture notes in Computer Science, vol. 4, pp. 715-731, January 2002.
Learning montages of transformed latent images as representations of objects that change in appearance (pdf)
C. Pal, B. J. Frey and N. Jojic
Proceedings of the European Conference on Computer Vision, Springer-Verlag lecture notes in Computer Science, 715-731,, January 2002.
Noise robust speech recognition using Gaussian basis functions for nonlinear likelihood function approximation (pdf)
C. Pal, B. J. Frey and T. T. Kristjansson
Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing, January 2002.
IEEE Operations Center, Piscataway, NJ.
Accounting for uncertainty in observations: A new paradigm for robust speech recognition (pdf)
T. T. Kristjansson, B. J. Frey and C. Pal
Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing, January 2002.
IEEE Operations Center, Piscataway, NJ.
Fast, large-scale transformation-invariant clustering (pdf)
B. J. Frey and N. Jojic
T. G. Dietterich, S. Becker, and Z. Ghahramani (eds) Advances in Neural Information Processing Systems 14, 721-728, January 2002.
MIT Press, Cambridge, MA.
Learning to model observations as products of hidden variables (pdf)
B. J. Frey, A. Kannan and N. Jojic
T. G. Dietterich, S. Becker, and Z. Ghahramani (eds) Advances in Neural Information Processing Systems 14, 729-736, January 2002.
MIT Press, Cambridge, MA.
Very loopy belief propagation for unwrapping phase images (pdf)
B. J. Frey, R. Koetter and N. Petrovic
In T. G. Dietterich, S. Becker, and Z. Ghahramani (eds) Advances in Neural Information Processing Systems 14, 737-744, January 2002.
MIT Press, Cambridge, MA.
ALGONQUIN – Learning dynamic noise models from noisy speech for robust speech recognition (pdf)
B. J. Frey, T. T. Kristjansson, L. Deng and A. Acero
In Dietterich, Becker, and Ghahramani (eds) Advances in Neural Information Processing Systems 14, 1165-1172, January 2002.
MIT Press, Cambridge, MA.
Noise Robust Speech Recognition Using Gaussian Basis Functions For Non-linear Likelihood Function Approximation (pdf)
Pal, C., Frey, B. and Kristjansson, T.
In the proceedings of IEEE ICASSP: International Conference on Acoustics Speech and Signal Processing, May 2002.
The Automated Extraction of Environmentally Relevant Features from Digital Imagery using Bayesian Multi-Resolution Analysis (pdf)
Pal, C. Swayne, D. and Frey, B.
Advances in Environmental Research. vol. 5, issue 4, pp 435-444 , January 2001.
Separating appearance from deformation (pdf)
N. Jojic, P. Simard, B. J. Frey and D. Heckerman
Proceedings of the IEEE International Conference on Computer Vision, Vol. II, 288-294, January 2001.
IEEE Computer Society Press, Los Alamitos, CA.
Sequentially fitting \"inclusive\" trees for inference in noisy-OR networks (pdf)
B. J. Frey, R. Petrascu, T. S. Jaakkola and J. Moran
T. K. Leen, T. G. Dietterich and V. Tresp (eds) Advances in Neural Information Processing Systems 13, 493-500, January 2001.
MIT Press, Cambridge, MA.
Keeping flexible active contours on track using Metropolis updates (pdf)
T. T. Kristjansson and B. J. Frey
T. K. Leen, T. G. Dietterich and V. Tresp (eds) Advances in Neural Information Processing Systems 13, 859-866, January 2001.
MIT Press, Cambridge, MA.
ALGONQUIN: Iterating Laplace’s method to remove multiple types of acoustic distortion for robust speech recognition (pdf)
B. J. Frey, L. Deng, A. Acero, T. T. Kristjansson
Proceedings of Eurospeech, 2001, January 2001.
Joint estimation of noise and channel distortion in a generalized EM framework (pdf)
T. T. Kristjansson, B. J. Frey, L. Deng and A. Acero
Proceedings of the IEEE Workshop on Automatic Speech Recognition and Understanding, 2001, January 2001.
Unwrapping phase images by propagating probabilities across graphs (pdf)
R. Koetter, B. J. Frey, N. Petrovic and D. C. Munson, Jr
Proceedings of the International Conference on Acoustics, Speech and Signal Processing, January 2001.
IEEE Operations Center, Piscataway, NJ.
Towards non-stationary noise adaptation for large vocabulary speech recognition systems (pdf)
T. T. Kristjansson, L. Deng, A. Acero, B. J. Frey
Proceedings of the International Conference on Acoustics, Speech and Signal Processing, January 2001.
IEEE Operations Center, Piscataway, NJ.
Unwrapping phases by relaxed mean field inference (pdf)
K. Achan, B. J. Frey, R. Koetter and D. C. Munson, Jr
Proceedings of the International Conference on Acoustics, Speech and Signal Processing, 1-6, January 2001.
IEEE Operations Center, Piscataway, NJ.
Factor graphs and the sum-product algorithm (pdf) (Shorter 1997 Conference Paper)
Frank R Kschischang, Brendan J Frey and Hans-A Loeliger
IEEE Transactions on Information Theory, Vol 47, No 2, pp 498-519, February 2001.
Introduction to the special issue on codes on graphs and iterative algorithms (pdf)
B. J. Frey, R. Koetter, G. D. Forney, Jr., F. R. Kschischang, R. J. McEliece and D. A. Spielman
IEEE Trans. Information Theory 47:2, 493-497, February 2001.
Learning flexible sprites in video layers (pdf)
N. Jojic and B. J. Frey
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, December 2001.
IEEE Computer Society Press, Los Alamitos, CA.
A Probabilistic Approach to Image Feature Extraction, Segmentation and Interpretation (pdf)
Pal, C.
Masters of Mathematics Thesis, University of Waterloo , January 2000.
Masters of Mathematics Thesis, University of Waterloo .
Topographic transformation as a discrete latent variable (pdf)
N. Jojic and B. J. Frey
S. A. Solla, T. K. Leen, K.-R. Mller (eds) Advances in Neural Information Processing Systems 12, 477-484, January 2000.
MIT Press, Cambridge, MA .
Transformed hidden Markov models: Estimating mixture models of images and inferring spatial transformations in video sequences (pdf)
N. Jojic, N. Petrovic, B. J. Frey and T. S. Huang
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Vol. II, 26-33, January 2000.
IEEE Computer Society Press, Los Alamitos, CA.
Event-coupled hidden Markov models (pdf)
T. Kristjansson, B. Frey, T.S. Huang
Proceedings of the 2000 IEEE International Conference on Multimedia and Expo, 385-388, January 2000.
IEEE Operations Center, Piscataway, NJ.
Topographic transformation as a discrete latent variable (pdf)
Nebojsa Jojic and Brendan J Frey
Advances in Neural Information Processing Systems (NIPS), MIT Press, 7 pages, June 2000.
Presented at the 1999 conference.
Image Interpretation and Segmentation with Hierarchical Probabilistic Models (jrnl)
Chris Pal, David Swayne, Brendan Frey
4th International Conference on Integrating GIS and Environmental Modeling (GIS/EM4): Problems, Prospects and Research Needs., September 2000.
Banff, Alberta, Canada, September 2 - 8, 2000..
Variational learning in nonlinear Gaussian belief networks (pdf)
Brendan J Frey and Geoffrey E Hinton
Neural Computation, Vol 11, No 1, pp 193-214, January 1999.
Leginon: A system for fully automated acquisition of 1000 electron micrographs per day (pdf)
C. S. Potter, H. Chu, B. J. Frey, C. Green, N. Kisseberth, T. J. Madden, K. L. Miller, K. Nahrstedt, J. Pulokas, A. Reilein, D. Tcheng, D. Weber and B. Carragher
Ultramicroscopy 77, 153–161, January 1999.
Variational learning in mixed-state dynamic graphical models (pdf)
V. Pavlovic, B. J. Frey and T. S. Huang
Proceedings of the Fifteenth Conference on Uncertainty in Artificial Intelligence, January 1999.
Morgan Kaufmann, San Francisco, CA. 8 pages.
A probabilistic framework for embedded face and facial expression recognition (pdf)
A. Colmenarez, B. J. Frey and T. S. Huang
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition 1999, January 1999.
IEEE Computer Society Press, Los Alamitos, CA.
Time-series classification using mixed-state dynamic Bayesian networks (pdf)
V. Pavlovic, B. J. Frey and T. S. Huang
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition 1999, Vol. II, 609-615, January 1999.
IEEE Computer Society Press, Los Alamitos, CA.
Embedded face and facial expression recognition (pdf)
A. Colmenarez, B. J. Frey and T. S. Huang
Proceedings of the IEEE International Conference on Image Processing 1999, 592-597, January 1999.
IEEE Operations Center, Piscataway, NJ.
Detection and tracking of faces and facial features (pdf)
A. Colmenarez, B. J. Frey and T. S. Huang
Proceedings of the IEEE International Conference on Image Processing 1999, 657-661, January 1999.
IEEE Operations Center, Piscataway, NJ.
Estimating mixture models of images and inferring spatial transformations using the EM algorithm (pdf)
Brendan J Frey and Nebojsa Jojic
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Ft. Collins, CO, 7 pages, June 1999.
Irregular turbocodes (pdf)
Brendan J Frey and David J C MacKay
Proceedings of the Allerton Conference on Communication, Control and Computing, Montecello, IL, 8 pages, June 1999.
Presented at the 1998 conference.
Estimating mixture models of images and inferring spatial transformations using the EM algorithm (pdf)
B. J. Frey and N. Jojic
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition 1999, 416-422, June 1999.
IEEE Computer Society Press, Los Alamitos, CA.
Transformed component analysis: Joint estimation of spatial transformations and image components (pdf)
Brendan J Frey and Nebojsa Jojic
Proceedings of the IEEE International Conference on Computer Vision, Kerkya, Greece, IEEE Computer Society Press, Los Alamitos, CA, 7 pages, September 1999.
Transformed component analysis: Joint estimation of spatial transformations and image components (pdf)
B. J. Frey and N. Jojic
Proceedings of the IEEE International Conference on Computer Vision 1999, 1190-1196, September 1999.
IEEE Computer Society Press, Los Alamitos, CA.
Graphical Models for Machine Learning and Digital Communication
Brendan J Frey
MIT Press, January 1998.
Iterative decoding of compound codes by probability propagation in graphical models (pdf)
Frank R Kschischang and Brendan J Frey
IEEE Journal on Selected Areas in Communications, Vol 16, pp 219-230, January 1998.
Probabilistic multimedia objects (MULTIJECTS): A novel approach to multimedia indexing and retrieval in digital systems (pdf)
M. Naphade, T. Kristjansson, B. J. Frey and T. S. Huang
Proceedings of the 1998 IEEE International Conference on Image Processing, 536-540, January 1998.
IEEE Operations Center, Piscataway, NJ.
Early detection and trellis splicing: Reduced-complexity iterative decoding (pdf)
Brendan J Frey and Frank R Kschischang
IEEE Journal on Selected Areas in Communications, Vol 16, pp 153-160, February 1998.
Early detection and trellis splicing: Reduced-complexity soft iterative decoding (pdf)
B. J. Frey, F. R. Kschischang and P. G. Gulak
T. Maseng (ed), Proceedings of the 1996 Turbo-coding Seminar, February 1998.
Lund, Sweden.
Markovian inference in belief networks (pdf)
B. J. Frey, C. M. Bishop and N. Lawrence
Proceedings of the Learning Workshop, Snowbird, Utah, Apr. 7 - 10, 1998, April 1998.
A revolution: Belief propagation in graphs with cycles (pdf)
Brendan J Frey and David J C MacKay
Advances in Neural Information Processing Systems (NIPS), June 1998.
Presented at the 1997 conference.
Trellis-constrained codes (pdf)
Brendan J Frey and David J C MacKay
Proceedings of the Allerton Conference on Communication, Control and Computing, Montecello, IL, 10 pages, June 1998.
Presented at the 1997 conference.
Mixtures of local linear subspaces for face recognition (pdf)
B. J. Frey
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition 1998, 32-37, June 1998.
Computer Society Press, Los Alamitos, CA.
Factor graphs and algorithms (pdf)
Brendan J Frey, Frank R Kschischang, Hans-A Loeliger, Niclas Wiberg
Proceedings of the Allerton Conference on Communication, Control and Computing, Montecello, IL, 8 pages, September 1998.
A simple algorithm that discovers efficient perceptual codes (pdf) (ps)
B. J. Frey, P. Dayan and G. E. Hinton
In M. Jenkin and L. R. Harris (editors), Computational and Psychophysical Mechanisms of Visual Coding. Cambridge University Press: New York, NY, January 1997.
Efficient stochastic source coding and an application to a Bayesian network source model (ps)
Brendan J Frey and Geoffrey E Hinton
The Computer Journal, Vol 40, pp 157-165, January 1997.
Continuous sigmoidal Bayesian networks trained using slice sampling (pdf)
B. J. Frey
M. C. Mozer, M. I. Jordan and T. Petsche (eds), Advances in Neural Information Processing Systems 9, 452-459, January 1997.
MIT Press, Cambridge MA.
Trellis-constrained codes (pdf)
B. J. Frey and D. J. C. MacKay
Proceedings of the 35th Allerton Conference on Communication, Control, and Computing, 691-700, Champaign-Urbana, IL, 1997, January 1997.
A simple algorithm that discovers efficient perceptual codes (pdf)
B. J. Frey, P. Dayan and G. E. Hinton
M. Jenkin and L. R. Harris (eds), Computational and Psychophysical Mechanisms of Visual Coding, January 1997.
Cambridge University Press, New York NY.
Factor graphs and algorithms (pdf)
B. J. Frey, F. R. Kschischang, H.-A. Loeliger and N. Wiberg
Proceedings of the 35th Allerton Conference on Communication, Control, and Computing, 666-680, January 1997.
Champaign- Urbana, IL.
Factor graphs and algorithms (pdf)
BJ Frey, FR Kschischang, H-A Loeliger, N Wiberg
Proc Allerton Conf on Communication, Control and Computing , January 1997.
Continuous sigmoidal belief networks trained using slice sampling (pdf)
Brendan J Frey
Advances in Neural Information Processing Systems (NIPS), June 1997.
Presented at the 1996 conference.
Variational learning in non-linear Gaussian belief networks (pdf)
B. J. Frey and G. E. Hinton
Neural Computation 11:1, 193–213, October 1997.
Does the wake-sleep algorithm produce good density estimators? (pdf)
B. J. Frey, G. E. Hinton and P. Dayan
In Advances in Neural Information Processing Systems (NIPS) , January 1996.
Probability propagation and iterative decoding (pdf)
B. J. Frey and F. R. Kschischang
Proceedings of the 34th Allerton Conference on Communication, Control, and Computing, January 1996.
Champaign-Urbana, IL.
Early detection and trellis splicing: Reduced-complexity iterative decoding (pdf)
B. J. Frey and F. R. Kschischang
IEEE Journal on Selected Areas in Communications 16:2, 153–159, August 1996.
Variational inference for continuous sigmoidal Bayesian networks (pdf)
B. J. Frey.
Sixth International Workshop on Artificial Intelligence and Statistics, November 1996.
Ft. Lauderdale, FL.
Using neural networks to monitor for rare failures (pdf)
G. E. Hinton and B. J. Frey
Proceedings of the 37th Mechanical Working and Steel Processing Conference 1995, January 1995.
Hamilton, ON.
The wake-sleep algorithm for unsupervised neural networks (pdf)
G. E. Hinton, P. Dayan, B. J. Frey and R. M. Neal
Science 268, 1158–1161, April 1995.