Publications

Large Language Models Are Human-Level Prompt Engineers (jrnl)
Yongchao Zhou, Andrei I. Muresanu, Ziwen Han, Keiran Paster, Silviu Pitis, Harris Chan, Jimmy Ba
International Conference on Learning Representations (ICLR), May 2023.

DynGFN: Bayesian Dynamic Causal Discovery using Generative Flow Networks (jrnl)
Lazar Atanackovic, Alexander Tong, Jason Hartford, Leo J. Lee, Bo Wang, Yoshua Bengio
arXiv preprint arXiv:2302.04178, February 2023.

Energy-based Modelling for Single-cell Data Annotation (jrnl)
Tianyi Liu, Philip Fradkin, Lazar Atanackovic, Leo J. Lee
Proceedings of the 17th Machine Learning in Computational Biology meeting, PMLR 200:94-109, December 2022.

Dataset distillation using neural feature regression (jrnl)
Yongchao Zhou, Ehsan Nezhadarya, Jimmy Ba
Neural Information Processing Systems (NeurIPS), December 2022.

Bayesian Dynamic Causal Discovery (jrnl)
Alexander Tong, Lazar Atanackovic, Jason Hartford, Yoshua Bengio
Neural Information Processing Systems (NeurIPS) A Causal View on Dynamical Systems Workshop, December 2022.

A graph neural network approach for molecule carcinogenicity prediction (jrnl)
Philip Fradkin, Adamo Young, Lazar Atanackovic, Brendan J. Frey, Leo J. Lee, and Bo Wang
Bioinformatics, 38(Supplement_1):i84-i91, July 2022.

RTfold: RNA secondary structure prediction using deep learning with domain inductive bias (jrnl)
Andrew J. Jung, Leo J. Lee, Alice J. Gao, Brendan J. Frey
International Conference on Learning Representations (ICML) Workshop on Computational Biology 2022 (Spotlight), July 2022.

Robustness to Adversarial Gradients: A Glimpse Into the Loss Landscape of Contrastive Pre-training (jrnl)
Philip Fradkin, Lazar Atanackovic, Michael R. Zhang
International Conference on Learning Representations (ICML) First Workshop on Pre-training: Perspectives, Pitfalls, and Paths Forward, July 2022.

A Novel Proteogenomic Integration Strategy Expands the Breadth of Neo-Epitope Sources (jrnl)
Haitao Xiang, Le Zhang, Fanyu Bu, Xiangyu Guan, Lei Chen, Haibo Zhang, Yuntong Zhao, Huanyi Chen, Weicong Zhang, Yijian Li, Leo J. Lee, Zhanlong Mei, Yuan Rao, Ying Gu, Yong Hou, Feng Mu, Xuan Dong
Cancers, 14(12), 3016, June 2022.

IntroSpect: Motif-Guided Immunopeptidome Database Building Tool to Improve the Sensitivity of HLA I Binding Peptide Identification by Mass Spectrometry (jrnl)
Le Zhang, Geng Liu, Guixue Hou, Haitao Xiang, Xi Zhang, Ying Huang, Xiuqing Zhang, Bo Li, and Leo J. Lee
Biomolecules, 12(4), p.579, April 2022.

Machine Learning Approaches for RNA Editing Prediction (pdf)
Andrew J. Jung, Leo J. Lee, Alice J. Gao and Brendan J. Frey
Machine Learning in Computational Biology (MLCB 2020), December 2020.

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction (jrnl)
Wells, Daniel K., et al.
Cell, 183(3), 818-834, October 2020.
(Leo J. Lee led the BGI team within the Tumor Neoantigen Selection Alliance)

The co-stimulation of anti-CD28 and IL-2 enhances the sensitivity of ELISPOT assays for detection of neoantigen-specific T cells in PBMC (jrnl)
Yunxia Tang, Linnan Zhu, Qumiao Xu, Xiuqing Zhang, Bo Li and Leo J. Lee
Journal of Immunological Methods, 484, 112831, September 2020.

HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps (pdf)
Michael C. Dimmick, Leo J. Lee and Brendan J. Frey
bioRXiv doi: https://doi.org/10.1101/2020.02.24.961714, July 2020.

ADAR1-Dependent RNA Editing Promotes MET and iPSC Reprogramming by Alleviating ER Stress (jrnl)
Diana Guallar, Alejandro Fuentes-Iglesias, Yara Souto, Cristina Ameneiro, Oscar Freire-Agulleiro, Jose Angel Pardavila, Adriana Escudero, Vera Garcia-Outeiral, Tiago Moreira, Carmen Saenz, Heng Xiong, Dongbing Liu, Shidi Xiao, Yong Hou, Kui Wu, Daniel Torrecilla, Jochen C. Hartner, Miguel G. Blanco, Leo J. Lee, Miguel López, Carl R. Walkley, Jianlong Wang, and Miguel Fidalg
Cell Stem Cell, doi:10.1016/j.stem.2020.04.016, May 2020.

ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping (jrnl)
Daniele Merico, Carl Spickett, Matthew O’Hara, Boyko Kakaradov, Amit G. Deshwar, Phil Fradkin, Shreshth Gandhi, Jiexin Gao, Solomon Grant, Ken Kron, Frank W. Schmitges, Zvi Shalev, Mark Sun, Marta Verby, Matthew Cahill, James J. Dowling, Johan Fransson, Erno Wienholds, and Brendan J. Frey
npj Genomic Medicine, doi:10.1038/s41525-020-0123-6, April 2020.

Memory-based graph networks (pdf)
Amir H. Khasahmadi, Kaveh Hassani, Parsa Moradi, Leo J. Lee and Quaid Morris
In International Conference on Learning Representations 2020, January 2020.

cDeepbind: A context sensitive deep learning model of RNA-protein binding (pdf)
Shreshth Gandhi, Leo J. Lee, Andrew Delong, David Duvenaud and Brendan J. Frey
Machine Learning in Computational Biology (MLCB 2019), December 2019.

HiCSR: A Hi-C Super-Resolution Framework for Producing Highly Realistic Contact Maps (pdf)
Michael C. Dimmick, Leo J. Lee and Brendan J. Frey
Machine Learning in Computational Biology (MLCB 2019), December 2019.

EPIP: MHC-I epitope prediction integrating mass spectrometry derived motifs and tissue-specific expression profiles (pdf)
Weipeng Hu, Si Qiu, Youping Li, Xinxin Lin, Le Zhang, Haitao Xiang, Xing Han, Lei Chen, Sha Li, Wenhui Li, Zhe Ren, GuiXue Hou, Zhilong Lin, Jianliang Lu, Geng Liu, Bo Li and Leo J. Lee
bioRXiv doi: https://doi.org/10.1101/567081, March 2019.

Deep learning in biomedicine (jrnl) (PubMed)
Michael Wainberg, Daniele Merico, Andrew Delong and Brendan J Frey
Nature Biotechnology, 36(9):829-838, September 2018.

COSSMO: predicting competitive alternative splice site selection using deep learning (jrnl) (PubMed)
Hannes Bretschneider, Shreshth Gandhi, Amit G Deshwar, Khalid Zuberi and Brendan J Frey
Bioinformatics, 34(13):i429-i437, July 2018.

cDeepbind: A context sensitive deep learning model of RNA-protein binding (pdf)
Shreshth Gandhi, Leo J. Lee, Andrew Delong, David Duvenaud and Brendan J. Frey
bioRXiv doi: https://doi.org/10.1101/345140, June 2018.

Inference of the Human Polyadenylation Code (jrnl) (PubMed)
Michael K K Leung, Andrew Delong and Brendan J Frey
Bioinformatics, bty211, https://doi.org/10.1093/bioinformatics/bty211, April 2018.

PixelGAN Autoencoders (pdf)
Alireza Makhzani, Brendan Frey
Advances in Neural Information Processing Systems (NIPS), December 2017.

Generating and designing DNA with deep generative models (pdf)
Nathan Killoran, Leo J. Lee, Andrew Delong, David Duvenaud, Brendan J. Frey
Machine Learning in Computational Biology Workshop at NIPS, December 2017.

Min-Max Propagation (pdf)
Christopher Srinivasa, Inmar Givoni, Siamak Ravanbakhsh and Brendan J. Frey
Advances in Neural Information Processing Systems (NIPS), December 2017.

Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism (jrnl) (PubMed)
Dwi U Kemaladewi, Eleonora Maino, Elzbieta Hyatt, Huayun Hou, Maylynn Ding, Kara M Place, Xinyi Zhu, Prabhpreet Bassi, Zahra Baghestani, Amit G Deshwar, Daniele Merico, Hui Y Xiong, Brendan J Frey, Michael D Wilson, Evgueni A Ivakine & Ronald D Cohn
Nature Medicine, doi:10.1038/nm.4367 , July 2017.
Nature Medicine, Vol 23, No 8, 984-989, August 2017.

RED-ML: a novel, effective RNA editing detection method based on machine learning (jrnl) (PubMed)
Heng Xiong*, Dongbing Liu*, Qiye Li, Mengyue Lei, Liqin Xu, Liang Wu, Zongji Wang, Shancheng Ren, Wangsheng Li, Min Xia, Lihua Lu, Haorong Lu, Yong Hou, Shida Zhu, Xin Liu, Yinghao Sun, Jian Wang, Huanming Yang, Kui Wu, Xun Xu@, and Leo J Lee@
Gigascience 6(5):1-8 | doi: 10.1093/gigascience/gix012, May 2017.
(*: joint first authors; @: corresponding authors).

Automated analysis of high‐content microscopy data with deep learning (jrnl) (PubMed)
Oren Z Kraus, Ben T Grys, Jimmy Ba, Yolanda Chong, Brendan J Frey, Charles Boone, and Brenda J Andrews
Molecular Systems Biology, 13(4):924 | DOI 10.15252/msb.20177551, April 2017.

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder (jrnl) (PubMed)
Ryan K C Yuen, Daniele Merico, Matt Bookman, Jennifer L Howe, Bhooma Thiruvahindrapuram, Rohan V Patel, Joe Whitney, Nicole Deflaux, Jonathan Bingham, Zhuozhi Wang, Giovanna Pellecchia, Janet A Buchanan, Susan Walker, Christian R Marshall, Mohammed Uddin, Mehdi Zarrei, Eric Deneault, Lia D’Abate, Ada J S Chan, Stephanie Koyanagi, Tara Paton, Sergio L Pereira, Ny Hoang, Worrawat Engchuan, Edward J Higginbotham, Karen Ho, Sylvia Lamoureux, Weili Li, Jeffrey R MacDonald, Thomas Nalpathamkalam, Wilson W L Sung, Fiona J Tsoi, John Wei, Lizhen Xu, Anne-Marie Tasse, Emily Kirby, William Van Etten, Simon Twigger, Wendy Roberts, Irene Drmic, Sanne Jilderda, Bonnie MacKinnon Modi, Barbara Kellam, Michael Szego, Cheryl Cytrynbaum, Rosanna Weksberg, Lonnie Zwaigenbaum, Marc Woodbury-Smith, Jessica Brian, Lili Senman, Alana Iaboni, Krissy Doyle-Thomas, Ann Thompson, Christina Chrysler, Jonathan Leef, Tal Savion-Lemieux, Isabel M Smith, Xudong Liu, Rob Nicolson, Vicki Seifer, Angie Fedele, Edwin H Cook, Stephen Dager, Annette Estes, Louise Gallagher, Beth A Malow, Jeremy R Parr, Sarah J Spence, Jacob Vorstman, Brendan J Frey, James T Robinson, Lisa J Strug, Bridget A Fernandez, Mayada Elsabbagh, Melissa T Carter, Joachim Hallmayer, Bartha M Knoppers, Evdokia Anagnostou, Peter Szatmari, Robert H Ring, David Glazer, Mathew T Pletcher & Stephen W Scherer
Nature Neuroscience, doi:10.1038/nn.4524, March 2017.

Characterization of RNA editome in primary and metastatic lung adenocarcinomas (jrnl) (PubMed)
Lihua Peng*, Leo J Lee*, Heng Xiong, Hong Su, Junhua Rao, Dakai Xiao, Jianxing He, Kui Wu, Dongbing Liu
Oncotarget, doi: 10.18632, December 2016.
(*: joint first authors).

Does conservation account for splicing patterns? (jrnl) (PubMed)
Michael Wainberg, Babak Alipanahi and Brendan Frey
BMC Genomics, 17(1):787, October 2016.

Genome-wide characteristics of de novo mutations in autism (jrnl) (PubMed)
Ryan KC Yuen, Daniele Merico, Hongzhi Cao, Giovanna Pellecchia, Babak Alipanahi, Bhooma Thiruvahindrapuram, Xin Tong, Yuhui Sun, Dandan Cao, Tao Zhang, Xueli Wu, Xin Jin, Ze Zhou, Xiaomin Liu, Thomas Nalpathamkalam, Susan Walker, Jennifer L Howe, Zhuozhi Wang, Jeffrey R MacDonald, Ada JS Chan, Lia D’Abate, Eric Deneault, Michelle T Siu, Kristiina Tammimies, Mohammed Uddin, Mehdi Zarrei, Mingbang Wang, Yingrui Li, Jun Wang, Jian Wang, Huanming Yang, Matt Bookman, Jonathan Bingham, Samuel S Gross, Dion Loy, Mathew Pletcher, Christian R Marshall, Evdokia Anagnostou, Lonnie Zwaigenbaum, Rosanna Weksberg, Bridget A Fernandez, Wendy Roberts, Peter Szatmari, David Glazer, Brendan J Frey, Robert H Ring, Xun Xu & Stephen W Scherer
NPJ Genome Medicine, doi:10.1038/npjgenmed.2016.27, August 2016.

Classifying and segmenting microscopy images with deep multiple instance learning (jrnl) (PubMed)
Oren Z. Kraus, Jimmy Lei Ba, Brendan J. Frey
Bioinformatics 32(12): i52-i59 | doi: 10.1093/bioinformatics/btw252, June 2016.

Adversarial Autoencoders (pdf)
Alireza Makhzani, Jonathon Shlens, Navdeep Jaitly, Ian Goodfellow, Brendan Frey
ICLR Workshop, May 2016.

Survey Propagation beyond Constraint Satisfaction Problems (pdf)
Christopher Srinivasa, Siamak Ravanbakhsh, Brendan Frey
Proceedings of the 19th International Conference on Artificial Intelligence and Statistics (AISTATS), May 2016.

Probabilistic estimation of short sequence expression using RNA-Seq data and the positional bootstrap (jrnl)
Hui Yuan Xiong, Leo J. Lee, Hannes Bretschneider, Jiexin Gao, Nebojsa Jojic, Brendan J. Frey
bioRxiv doi: http://dx.doi.org/10.1101/046474, April 2016.

Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine (jrnl)
Dimitri J Stavropoulos, Daniele Merico, Rebekah Jobling, Sarah Bowdin, Nasim Monfared, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Giovanna Pellecchia, Ryan K C Yuen, Michael J Szego, Robin Z Hayeems, Randi Zlotnik Shaul, Michael Brudno, Marta Girdea, Brendan Frey, Babak Alipanahi, Sohnee Ahmed, Riyana Babul-Hirji, Ramses Badilla Porras, Melissa T Carter, Lauren Chad, Ayeshah Chaudhry, David Chitayat, Soghra Jougheh Doust, Cheryl Cytrynbaum, Lucie Dupuis, Resham Ejaz, Leona Fishman, Andrea Guerin, Bita Hashemi, Mayada Helal, Stacy Hewson, Michal Inbar-Feigenberg, Peter Kannu, Natalya Karp, Raymond H Kim, Jonathan Kronick, Eriskay Liston, Heather MacDonald, Saadet Mercimek-Mahmutoglu, Roberto Mendoza-Londono, Enas Nasr, Graeme Nimmo, Nicole Parkinson, Nada Quercia, Julian Raiman, Maian Roifman, Andreas Schulze, Andrea Shugar, Cheryl Shuman, Pierre Sinajon, Komudi Siriwardena, Rosanna Weksberg, Grace Yoon, Chris Carew, Raith Erickson, Richard A Leach, Robert Klein, Peter N Ray, M Stephen Meyn, Stephen W Scherer, Ronald D Cohn & Christian R Marshall
npj Genomic Medicine, vol. 1, Article number: 15012, doi:10.1038/npjgenmed.2015.12, January 2016.

Computer vision for high content screening (jrnl) (PubMed)
Oren Z. Kraus and Brendan J. Frey
Critical Reviews in Biochemistry and Molecular Biology, Epub ahead of print, January 2016.

Classifying Microscopy Images Using Convolutional Multiple Instance Learning (pdf)
Oren Z. Kraus, Jimmy Lei Ba, Brendan J. Frey
Machine Learning in Computational Biology Workshop at NIPS, December 2015.

Winner-Take-All Autoencoders (pdf)
Alireza Makhzani, Brendan Frey
Advances in Neural Information Processing Systems (NIPS), December 2015.

Learning Wake-Sleep Recurrent Attention Models (pdf) (jrnl)
Jimmy Lei Ba, Roger Grosse, Ruslan Salakhutdinov, Brendan J Frey
Advances in Neural Information Processing Systems (NIPS), December 2015.

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets (pdf) (jrnl)
Michael K. K. Leung, Andrew Delong, Babak Alipanahi, and Brendan J. Frey
Proceedings of the IEEE, DOI: 10.1109/JPROC.2015.2494198, December 2015.
Proceedings of the IEEE, Vol 104, No 1, January 2016.

Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome (jrnl) (PubMed)
Daniele Merico, Mehdi Zarrei, Gregory Costain, Lucas Ogura, Babak Alipanahi, Matthew J. Gazzellone, Nancy J. Butcher, Bhooma Thiruvahindrapuram, Thomas Nalpathamkalam, Eva W. C. Chow, Danielle M. Andrade, Brendan J. Frey, Christian R. Marshall, Stephen W. Scherer and Anne S. Bassett
G3: Genes, Genomes, Genetics, Vol 5, No 11, 2453-61, November 2015.

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning (jrnl) (PubMed)
Babak Alipanahi*, Andrew Delong*, Matthew T Weirauch and Brendan J Frey@
Nature Biotechnology, 33, 831-838 | doi:10.1038/nbt.3300, July 2015.
(*: joint first authors; @: corresponding author).

C2H2 zinc finger proteins greatly expand the human regulatory lexicon (jrnl) (PubMed)
Hamed S Najafabadi, Sanie Mnaimneh, Frank W Schmitges, Michael Garton, Kathy N Lam, Ally Yang, Mihai Albu, Matthew T Weirauch, Ernest Radovani, Philip M Kim, Jack Greenblatt, Brendan J Frey and Timothy R Hughes
Nature Biotechnology 33, 555–562 | doi:10.1038/nbt.3128, February 2015.

The human splicing code reveals new insights into the genetic determinants of disease (jrnl) (PubMed)
Hui Y. Xiong*, Babak Alipanahi*, Leo J. Lee*, Hannes Bretschneider, Daniele Merico, Ryan K. C. Yuen, Yimin Hua, Serge Gueroussov, Hamed S. Najafabadi, Timothy R. Hughes, Quaid Morris, Yoseph Barash, Adrian R. Krainer, Nebojsa Jojic, Stephen W. Scherer, Benjamin J. Blencowe, Brendan J. Frey@
Science Express, DOI: 10.1126/science.1254806, December 2014.
Science, Vol. 347, No. 6218, January 2015 (*: joint first authors; @: corresponding author).

Analysis of cryptic splice sites with deep convolutional networks (pdf)
Hannes Bretschneider, Babak Alipanahi, Leo J Lee, and Brendan J Frey
Machine Learning in Computational Biology Workshop at NIPS 2014, December 2014.

Deep learning of the tissue-regulated splicing code (pdf) (jrnl)
Michael K. K. Leung, Hui Yuan Xiong, Leo J. Lee, Brendan J. Frey
Proceedings of the 22nd Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), June 2014.
Bioinformatics, Vol 30, No. 12, i121-i129.

Min-Max Problems on Factor Graphs (pdf)
Siamak Ravanbakhsh, Christopher Srinivasa, Brendan Frey, Russell Greiner
International Conference on Machine Learning (ICML) 2014, June 2014.

k-Sparse Autoencoders (pdf)
Alireza Makhzani, Brendan Frey
International Conference on Learning Representations (ICLR), April 2014.

A convolutional model of RNA-binding proteins
Andrew Delong, Babak Alipanahi, Brendan J. Frey
NIPS Workshop on Machine Learning in Computational Biology, December 2013.

Adaptive dropout for training deep neural networks (pdf)
Jimmy Lei Ba, Brendan Frey
Advances in Neural Information Processing Systems 2013, December 2013.

AVISPA: a web tool for the prediction and analysis of alternative splicing (jrnl) (PubMed)
Yoseph Barash@, Jorge Vaquero-Garcia, Juan González-Vallinas, Hui Yuan Xiong, Weijun Gao, Leo J Lee and Brendan J Frey
Genome Biology, 14:R114, October 2013.
@: corresponding author.

Network cleanup (jrnl) (PubMed)
Babak Alipanahi and Brendan J Frey
Nature Biotechnology 31, 714–715, August 2013.

A compendium of RNA-binding motifs for decoding gene regulation (jrnl) (PubMed)
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 D. Morris & Timothy R. Hughes
Nature, Vol 499, No. 7457, July 2013.

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming (jrnl) (PubMed)
Hong Han, Manuel Irimia, P. Joel Ross, Hoon-Ki Sung, Babak Alipanahi, Laurent David, Azadeh Golipour, Mathieu Gabut, Iacovos P. Michael, Emil N. Nachman, Eric Wang, Dan Trcka, Tadeo Thompson, Dave O’Hanlon, Valentina Slobodeniuc, Nuno L. Barbosa-Morais, Christopher B. Burge, Jason Moffat, Brendan J. Frey, Andras Nagy, James Ellis, Jeffrey L. Wrana & Benjamin J. Blencowe
Nature, Vol 498, No. 7453, June 2013.

Mutations in STAMBP, encoding a deubiquitinating enzyme, cause microcephaly–capillary malformation syndrome (jrnl) (PubMed)
Laura M McDonell, Ghayda M Mirzaa, Diana Alcantara, Jeremy Schwartzentruber, Melissa T Carter, Leo J Lee, Carol L Clericuzio, John M Graham Jr, Deborah J Morris-Rosendahl, Tilman Polster, Gyula Acsadi, Sharron Townshend, Simon Williams, Anne Halbert, Bertrand Isidor, Albert David, Christopher D Smyser, Alex R Paciorkowski, Marcia Willing, John Woulfe, Soma Das, Chandree L Beaulieu, Janet Marcadier, FORGE Canada Consortium, Michael T Geraghty, Brendan J Frey, Jacek Majewski, Dennis E Bulman, William B Dobyns, Mark O’Driscoll, and Kym M Boycott
Nature Genetics, 2013 Mar 31. doi: 10.1038/ng.2602. [Epub ahead of print], March 2013.

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry (pdf)
Clement Chung, Andrew Emili and Brendan J Frey
Bioinformatics, Epub ahead of print, March 2013.

Probabilistic n-choose-k models for classification and ranking (pdf)
K. Swersky, D. Tarlow, R. Adams, R. Zemel, B. J. Frey
Advances in Neural Information Processing Systems (NIPS), December 2012.

The evolutionary landscape of alternative splicing in vertebrate species (jrnl) (PubMed)
Nuno L. Barbosa-Morais, Manuel Irimia, Qun Pan, Hui Y. Xiong, Serge Gueroussov, Leo J. Lee, Valentina Slobodeniuc, Claudia Kutter, Stephen Watt, Recep Çolak, TaeHyung Kim, Christine M. Misquitta-Ali, Michael D. Wilson, Philip M. Kim, Duncan T. Odom, Brendan J. Frey, and Benjamin J. Blencowe
Science 338(6114): 1587-1593, December 2012.

Fast exact inference for recursive cardinality models (pdf)
D. Tarlow, K. Swersky, R. Zemel. R. Adams, B. J. Frey
The 28th Conference on Uncertainty in Artificial Intelligence (UAI), July 2012.

Factorizing appearance using epitomic flobject analysis (pdf)
PS Li, BJ Frey
IEEE International Conference on Computer Vision and Pattern Recognition (CVPR), June 2012.

Learning structural element patch models with hierarchical palettes (pdf)
J Chua, I Givoni, RP Adams, BJ Frey
IEEE Conference on Computer Vision and Pattern Recognition (CVPR), June 2012.

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data (pdf)
B Kakaradov, H Xiong, LJ Lee, N Jojic, BJ Frey
BMC Bioinformatics 13, April 2012.

Beyond Affinity Propagation: Message Passing Algorithms for Clustering (pdf)
Inmar E. Givoni
PhD Thesis, December 2011.

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context (pdf)
Hui Y Xiong*, Yoseph Barash*, Brendan J Frey
Bioinformatics 27 (18), pg. 2554-2562, September 2011.
* Joint first authors.

Transcriptional Profiling of Endocrine Cerebro-Osteodysplasia Using Microarray and Next-Generation Sequencing (jrnl)
Piya Lahiry, Leo J. Lee, Brendan J. Frey, C. Anthony Rupar, Victoria M. Siu, Benjamin J. Blencowe, Robert A. Hegele
PLoS ONE 6(9): e25400. doi:10.1371/journal.pone.0025400, September 2011.

Matching Unstructured Product Offers to Structured Product Specifications (pdf)
Anitha Kannan, Inmar E. Givoni, Rakesh Agrawal, and Ariel Fuxman
The 17th ACM SIGKDD Conference on Knowledge Discovry and Data Mining KDD, August 2011.

Graph Cuts is a Max-Product Algorithm (pdf)
Daniel Tarlow, Inmar E. Givoni, Rich S. Zemel, and Brendan J. Frey
Uncertainty in Artificial Intelligence (UAI), July 2011.
Best Student Paper Award – Runner Up.

Hierarchical Affinity Propagation (pdf)
Inmar E. Givoni, Clement Chung, Brendan J. Frey
Uncertainty in Artificial Intelligence (UAI), July 2011.

Bayesian painting by numbers: Flexible priors for colour-invariant object recognition (pdf)
Jeroen C. Chua, Inmar E. Givoni, Ryan P. Adams, Brendan J. Frey
University of Toronto Technical Report PSI TR 2011-001, June 2011.

Learning Better Image Representations Using ‘Flobject Analysis’ (pdf)
Patrick S. Li*, Inmar E. Givoni*, Brendan J. Frey
IEEE Conference on Computer Vision and Pattern Recognition (CVPR), June 2011.
* Joint first authors.

STORMSeq: A Method for Ranking Regulatory Sequences by Integrating Experimental Datasets with Diverse Computational Predictions (jrnl)
Jim C Huang and Brendan J Frey
In H H-S Lu, B Scholkopf, H Zhao (eds), Handbook of Statistical Bioinformatics, Springer, 2011., May 2011.

Computational refinement of post-translational modifications predicted from tandem mass spectrometry (PubMed)
Chung C*, Liu J, Emili A, Frey BJ
Bioinformatics. Vol 27, No. 6, Pages 797-806, March 2011.
(*): first author
.

Genome-wide analysis of alternative splicing in Caenorhabditis elegans (jrnl) (PubMed)
Arun K. Ramani, John A. Calarco, Qun Pan, Sepand Mavandadi, Ying Wang, Andrew C. Nelson, Leo J. Lee, Quaid Morris, Benjamin J. Blencowe, Mei Zhen and Andrew G. Fraser
Genome Research, 21(2):342-348, February 2011.

Cumulative distribution networks and the derivative-sum-product algorithm: Models and inference for cumulative distribution functions on graphs (pdf)
Jim C Huang and Brendan J Frey
JMLR, Vol 12, 301-348, January 2011.

An illuminated view of molecular biology (jrnl)
Yoseph Barash, Xinchen Wang
Genome Biology , 11:307, August 2010, August 2010.

Model-based detection of alternative splicing signals (jrnl)
Yoseph Barash, Benjamin J. Blencowe, and Brendan J. Frey
Bioinformatics, Vol. 26 p. i325-333, 2010, July 2010.

Kernel-based Copula Processes (pdf)
Eddie K. H. Ng
Ph.D Thesis, June 2010.

Solving the Uncapacitated Facility Location Problem Using Message Passing Algorithms (pdf)
Nevena Lazic, Brendan J. Frey, Parham Aarabi
Proc. of the 13th International Conference on Artificial Intelligence and Statistics (AISTATS), May 2010.

Deciphering the splicing code (pdf) (jrnl)
Yoseph Barash, John A. Calarco, Weijun Gao, Qun Pan, Xinchen Wang, Ofer Shai, Benjamin J. Blencowe & Brendan J. Frey
Nature, 465:7294, pp53-59, May 2010.

HOP-MAP: Efficient Message Passing with High Order Potentials (pdf)
Daniel Tarlow, Inmar E. Givoni, Richard S. Zemel
Proceedings of the 13th International Conference on Artificial Intelligence and Statistics (AISTATS), May 2010, Sardinia., May 2010.

Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis
F. J. Vizeacoumar, N. van Dyk, V. Cheung, J. Li, Y. Sydorskyy, N. Case, Z. Li, A. Datti, C. Nislow, B. Raught, Z. Zhang, B. J. Frey, K. Bloom, C. Boone, B. J. Andrews
Journal of Cell Biology 188:1, 69-81, January 2010.

Cumulative distribution networks: Inference, estimation and applications of graphical models for cumulative distribution functions (pdf)
Jim C. Huang
PhD Thesis, November 2009.

Machine Learning in Computational Biology: Models of Alternative Splicing (pdf)
Ofer Shai
PhD Dissertation, University of Toronto, October 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.

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.

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.

Affinity Propagation: Clustering Data by Passing Messages (pdf)
Dueck, Delbert
University of Toronto Ph.D. thesis, June 2009.

Semi-Supervised Affinity Propagation with Instance-Level Constraints (pdf)
Inmar E. Givoni, Brendan J. Frey
Proceedings of the 12th International Conference on Artificial Intelligence and Statistics (AISTATS), April 2009.

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).

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.

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.

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)..

Fast transformation-invariant component analysis (pdf)
A. Kannan, N. Jojic, B. J. Frey
International Journal of Computer Vision 77:1, 87-101, May 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.

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.

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.

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, January 2008.

AFFINITY PROPAGATION and the VERTEX SUBSTITUTION HEURISTIC (jrnl)
Brendan J. Frey, Delbert Dueck
January 2008., 2008.

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.

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.

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).

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.

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.

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.

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.

Clustering by passing messages between data points (pdf)
Brendan J. Frey and Delbert Dueck
Science, Vol 315, No 5814, pp 972-976, February 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.

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.

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.

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.

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.

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.

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.

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.

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.

Detecting microRNA targets by linking sequence, microRNA and gene expression data (pdf)
J.C. Huang, Q.D. Morris and B.J. Frey
Lecture Notes in Computer Science, Springer-Verlag, 3909: 114-129, April 2006.

GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data (pdf)
B. J. Frey, T. R. Hughes and Q. D. Morris
JOURNAL OF COMPUTATIONAL BIOLOGY Volume 13, Number 2, March 2006.

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, March 2006.

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.

Alternative splicing of conserved exons is frequently species-specific in human and mouse (pdf)
Q. Pan, M. A. Bakowski, Q. Morris,W. Zhang, B. J. Frey, T. R. Hughes and B. J. Blencowe
TRENDS in Genetics Vol.21 No.2, February 2006.

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).

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).

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.

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.

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 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.

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.

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.

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.

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).

Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model (pdf)
B. J. Frey, Q. D. Morris, M. Robinson, T. R. Hughes
Proc. Ninth International Conference on Research in Computational Molecular Biology, RECOMB, 66-82, May 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.

Focused Inference (pdf) (ps)
Rómer Rosales and Tommi Jaakkola
In Artificial Intelligence and Statistics (AISTATS). Jan 2005, January 2005.

Learning Rankings via Convex Hull Separation (pdf)
Glenn Fung, Rómer Rosales, and Balaji Krishnapuram
In Proc. Neural Information Processing Systems (NIPS) 2005, January 2005.

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.

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.

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.

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) (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.

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.

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 sparse matrix factorization (pdf)
D. Dueck, B. J. Frey
University of Toronto Technical Report PSI-2004-23, September 2004.

Learning to Cluster using Local Neighborhood Structure (pdf) (ps)
Rómer Rosales, Kannan Achan, and Brendan Frey
In Proc. International Conference on Machine Learning (ICML). Jul 2004., July 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.

Gene function prediction using mouse gene expression profiles
Q. Morris, B. J. Frey and O. Shai
Proceedings of the Learning Workshop, Snowbird, UT, April 2004.

Graphical models for rational design of AIDS vaccine cocktails
N. Jojic, V. Jojic, B. J. Frey, C. Meek and D. Heckerman
Proceedings of the Learning Workshop, Snowbird, UT, April 2004.

Learning ‘epitomes’ of array data
B. J. Frey and N. Jojic
Proceedings of the Learning Workshop, Snowbird, UT, April 2004.

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 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.

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.

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.

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.

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.

Extending factor graphs so as to unify directed and undirected graphical models (pdf)
B. J. Frey
Proceedings of the 19th Conference on Uncertainty in Artificial Intelligence, 257-264, Morgan Kaufmann, San Francisco, CA, August 2003.

Learning Generative Models of Similarity Matrices (pdf)
Rómer Rosales and Brendan Frey
In Proc. 19th Conference on Uncertainty in Artificial Intelligence (UAI). Aug 2003., August 2003.

Learning appearance and transparency manifolds of occluded objects in layers (pdf)
BJ Frey, N Jojic, A Kanan
IEEE CVPR 2003, June 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.

Probabilistic block clustering
S. T. Roweis, C. J. Pal, Q. Morris and B. J. Frey
Proceedings of the Learning Workshop, Snowbird, UT, April 2003.

Bayesian belief networks
B. J. Frey
Encyclopedia of Cognitive Science, Nature Publishing Group, January 2003.

Transformation-Invariant Clustering Using the EM Algorithm (pdf)
B. J. Frey and N. Jojic
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, VOL. 25, NO. 1, 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 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.

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.

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.

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.

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 the “Epitome” of an Image (pdf)
Brendan J. Frey and Nebojsa Jojic
University of Toronto TR PSI-2002-14, November 2002.

Phase unwrapping by minimizing Kikuchi free energy (pdf)
K. Achan, B. J. Frey, R. Koetter and D. C. Munson
Proceedings of the International Geoscience & Remote Sensing Symposium, IEEE Geoscience and Remote Sensing Society Press, Los Alamitos, CA, June 2002.

Learning layered models of occluding objects
B. J. Frey and N. Jojic
Proceedings of the Learning Workshop, Snowbird, UT, April 2002.

Balancing rewrapping error and smoothness in two-dimensional phase unwrapping problems
D. Schultz, R. Koetter, B. J. Frey and D. Munson
Proceedings of the International Geoscience & Remote Sensing Symposium, IEEE Geoscience and Remote Sensing Society Press, Los Alamitos, CA, February 2002.

Product analysis: Learning to model observations as products of hidden variables (pdf) (ps)
B. J. Frey, A. Kannan and N. Jojic
Advances in Neural Information Processing Systems 14, 729-736, MIT Press, Cambridge, MA, January 2002.

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.

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.

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.

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.

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.

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.

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 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.

Phase unwrapping using the sum-product algorithm
B. J. Frey, R. Koetter and N. Petrovic
Proceedings of the IEEE Information Theory Workshop, IEEE Operations Center, Piscataway, NJ, February 2001.

Signal space characterization of iterative decoding (pdf)
B. J. Frey, R. Koetter and A. Vardy
IEEE Trans. Information Theory 47:2, 766-781, 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.

Factor graphs and the sum-product algorithm (pdf)
Frank R Kschischang, Brendan J Frey and Hans-A Loeliger
IEEE Transactions on Information Theory, Vol 47, No 2, pp 498-519, February 2001.

Knowing when to stop
B. J. Frey
Proceedings of the 38th Allerton Conference on Communication, Control, and Computing, Champaign-Urbana, IL, January 2001.

Estimating smooth deformation models of substance and noise (pdf)
N. Jojic, P. Simard B. J. Frey and D. Heckerman
Proceedings of the Eighth International Workshop on Artificial Intelligence and Statistics, 214- 219, January 2001.

Accumulator networks: Suitors of local probability propagation (pdf)
B. J. Frey and A. Kannan
Advances in Neural Information Processing Systems 13, 486-493, MIT Press, Cambridge, MA, January 2001.

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.

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 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.

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.

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.

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.

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.

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.

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.

Transformation-invariant filtering using expectation maximization
B. J. Frey
Proceedings of Symposium 2000 on Adaptive Systems for Signal Processing, Communications and Control, 19-24, Chateau Lake Louise, AB, October 2000.

Irregular turbo-like codes
B. J. Frey and D. J. C. MacKay
Proceedings of the 2nd International Symposium on Turbocodes and Related Topics, 67-72, Brest, France, September 2000.

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..

A new block-coded modulation scheme for Rayleigh fading channels (pdf)
S. Yousefi, E. S. Hons, A. K. Khandani and B. J. Frey
Proceedings of the IEEE International Symposium on Information Theory, 249, IEEE Operations Center, Piscataway, NJ, June 2000.

Filling In Scenes by Propagating Probabilities through Layers and Into Appearance Models
Brendan J. Frey
2000 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR’00) – Volume 1, June 2000.

Learning to segment coherent image components by constraining and abusing factor analysis
B. J. Frey
Proceedings of the Learning Workshop, Snowbird, UT, April 2000.

Attenuated max-product propagation finds the maximum a posteriori solution
B. J. Frey and R. Koetter
Advanced Mean Field Methods:Theory and Practice, MIT Press, Cambridge, MA, January 2000.

Learning sparse multiple cause models
M. R. Naphade, L. S. Chen, T. S. Huang and B. J. Frey
Proceedings of the IEEE International Conference on Pattern Recognition, 2642-2647, IEEE Operations Center, Piscataway, NJ, January 2000.

A convergence theorem for iterative decoding
R. Koetter and B. J. Frey
Proceedings of the 2000 IEEE International Symposium on Information Theory and its Applications, 121, IEEE Operations Center, Piscataway, NJ, January 2000.

Integrating statistical methodologies in automated image analysis systems
C. Pal, B. J. Frey and D. Swayne
Proceedings of the International Symposium for Environmental Software Systems, January 2000.

Learning graphical models of images, videos and their spatial transformations
B. J. Frey and N. Jojic
Proceedings of the Sixteenth Conference on Uncertainty in Artificial Intelligence, 184-191, Morgan Kaufmann, San Francisco, CA, January 2000.

Loopy probability propagation for factor analysis
B. J. Frey
Advances in Neural Information Processing Systems 12, 442-449, MIT Press, Cambridge, MA, January 2000.

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.

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.

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 .

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 .

Variational inference for continuous sigmoidal Bayesian networks (pdf)
B. J. Frey
Sixth International Workshop on Artificial Intelligence and Statistics, November 1996.
Ft. Lauderdale, FL.

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.

Object-based expert systems in integrated power system analysis
R. Wheatley, B. J. Frey, G. S. Hope and O. P. Malik
Proceedings of the 1989 Canadian Conference on Electrical and Computer Engineering, September 1989.

Skewness and pseudocodewords in iterative decoding
B. J. Frey, R. Koetter and A. Vardy
In Proceedings of the 1998 IEEE International Symposium on Information Theory, 148, IEEE Operations Center, Piscataway, NJ, August 1998.

Early detection and trellis splicing: Reduced-complexity soft iterative decoding (pdf)
B. J. Frey and F. R. Kschischang
IEEE Journal on Selected Areas in Communications 16:2, 153–159, August 1996.

Distributed QoS-aware high performance environment for support of automated TEM
K. Nahrstedt, H. Chu, C. Lin, C. S. Potter, N. Kisseberth, B. Carragher, B. J. Frey, K. L. Miller and R. Josephs
Proceedings of the 7th IEEE Symposium on High Performance Distributed Computing (HPDC-7), Chicago, IL, July 1998.

Filtering with factor graphs: Kalman filtering and beyond
B. J. Frey
Proceedings of the Workshop on Mathematical Theory of Networks and Systems, Padova, Italy, July 1998.

A testbed for automated acquisition from a TEM
C. S. Potter, B. Carragher, H. Chu, B. J. Frey, R. Josephs, C. Lin, N. Kisseberth, K.L. Miller and K. Nahrstedt
Proceedings of Microscopy and Microanalysis 1998, Atlanta, July 1998.

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.

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.

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.

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.

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.

Pseudo-random codes based on Bayesian networks
B. J. Frey
1997 CanadianWorkshop on Information Theory, Toronto, ON, June 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.

Concurrent turbodecoding
B. J. Frey, F. R. Kschischang and P. G. Gulak
Proceedings of the 1997 IEEE International Symposium on Information Theory, 431, IEEE Operations Center, Piscataway, NJ, May 1997.

An FPGA implementation of a robotic airship controller
B. J. Frey, D. C. Blight and A. McIlraith
The First Canadian Workshop on Field Programmable Devices,Winnipeg MA, May 1993.

Transformed mixtures of Gaussians
B. J. Frey and N. Jojic
Proceedings of the Learning Workshop, Snowbird, UT, April 1999.

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.

Free energy coding
B. J. Frey and G. E. Hinton
Proceedings of the Data Compression Conference 1996, 73-81, IEEE Computer Society Press, Los Alamitos, CA, April 1996.

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.

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.

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.

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.

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.

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.

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.

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 nonlinear Gaussian belief networks (pdf)
Brendan J Frey and Geoffrey E Hinton
Neural Computation, Vol 11, No 1, pp 193-214, January 1999.

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.

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.

Graphical Models for Machine Learning and Digital Communication
Brendan J Frey
MIT Press, January 1998.

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.

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.

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.

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.

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.

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.

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.