Brendan Frey
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Brendan Freycomputer-science Degrees
Computer Science
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Machine Learning
#54
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#54
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Algorithms
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Brendan Freyengineering Degrees
Engineering
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Cybernetics
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#48
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Electrical Engineering
#857
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Computer Science Engineering
Why Is Brendan Frey Influential?
(Suggest an Edit or Addition)According to Wikipedia, Brendan John Frey FRSC is a Canadian-born entrepreneur, engineer and scientist. He is Founder and CEO of Deep Genomics, Cofounder of the Vector Institute for Artificial Intelligence and Professor of Engineering and Medicine at the University of Toronto. Frey is a pioneer in the development of machine learning and artificial intelligence methods, their use in accurately determining the consequences of genetic mutations, and in designing medications that can slow, stop or reverse the progression of disease.
Brendan Frey's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Clustering by Passing Messages Between Data Points (2007) (6242)
- Factor graphs and the sum-product algorithm (2001) (4836)
- Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing (2008) (3395)
- Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning (2015) (2041)
- A compendium of RNA-binding motifs for decoding gene regulation (2013) (1214)
- The "wake-sleep" algorithm for unsupervised neural networks. (1995) (1057)
- The human splicing code reveals new insights into the genetic determinants of disease (2015) (1040)
- The Evolutionary Landscape of Alternative Splicing in Vertebrate Species (2012) (870)
- Deciphering the splicing code (2010) (834)
- Graphical Models for Machine Learning and Digital Communication (1998) (635)
- Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder (2017) (575)
- Widespread intron retention in mammals functionally tunes transcriptomes (2014) (500)
- Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast (2006) (484)
- Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling (2006) (470)
- Iterative Decoding of Compound Codes by Probability Propagation in Graphical Models (1998) (437)
- Using expression profiling data to identify human microRNA targets (2007) (424)
- Deep learning of the tissue-regulated splicing code (2014) (396)
- A Revolution: Belief Propagation in Graphs with Cycles (1997) (387)
- Classifying and segmenting microscopy images with deep multiple instance learning (2015) (356)
- Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. (2004) (350)
- The functional landscape of mouse gene expression (2004) (341)
- Deep learning in biomedicine (2018) (336)
- Non-metric affinity propagation for unsupervised image categorization (2007) (336)
- Adaptive dropout for training deep neural networks (2013) (320)
- Learning flexible sprites in video layers (2001) (295)
- MBNL proteins repress ES-cell-specific alternative splicing and reprogramming (2013) (286)
- Epitomic analysis of appearance and shape (2003) (270)
- A Panoramic View of Yeast Noncoding RNA Processing (2003) (269)
- C2H2 zinc finger proteins greatly expand the human regulatory lexicon (2015) (266)
- Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine (2016) (249)
- Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression. (2006) (240)
- Transformation-Invariant Clustering Using the EM Algorithm (2003) (215)
- Winner-Take-All Autoencoders (2014) (215)
- Probabilistic multimedia objects (multijects): a novel approach to video indexing and retrieval in multimedia systems (1998) (213)
- Automated analysis of high‐content microscopy data with deep learning (2017) (212)
- A comparison of algorithms for inference and learning in probabilistic graphical models (2005) (202)
- Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets (2016) (199)
- Identifying transcription factor functions and targets by phenotypic activation (2006) (195)
- Genome-wide characteristics of de novo mutations in autism (2016) (195)
- Video Epitomes (2005) (169)
- Alternative splicing of conserved exons is frequently species-specific in human and mouse. (2005) (166)
- A Binary Variable Model for Affinity Propagation (2009) (148)
- Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder (2014) (144)
- Are Random Forests Truly the Best Classifiers? (2016) (133)
- Bayesian Inference of MicroRNA Targets from Sequence and Expression Data (2007) (125)
- Functional coordination of alternative splicing in the mammalian central nervous system (2007) (120)
- ALGONQUIN: iterating laplace's method to remove multiple types of acoustic distortion for robust speech recognition (2001) (119)
- Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis (2010) (116)
- Stel component analysis: Modeling spatial correlations in image class structure (2009) (115)
- Generating and designing DNA with deep generative models (2017) (112)
- Mixture Modeling by Affinity Propagation (2005) (107)
- Comparative Proteomics Profiling of a Phospholamban Mutant Mouse Model of Dilated Cardiomyopathy Reveals Progressive Intracellular Stress Responses*S (2008) (106)
- Multi-way clustering of microarray data using probabilistic sparse matrix factorization (2005) (102)
- Mutations in STAMBP, encoding a deubiquitinating enzyme, cause Microcephaly-Capillary Malformation syndrome (2013) (99)
- Factor Graphs and Algorithms (2008) (98)
- 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. (2008) (95)
- Estimating mixture models of images and inferring spatial transformations using the EM algorithm (1999) (93)
- Transformed component analysis: joint estimation of spatial transformations and image components (1999) (91)
- Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context (2011) (90)
- FLoSS: Facility location for subspace segmentation (2009) (87)
- Hierarchical Affinity Propagation (2011) (86)
- Extending Factor Graphs so as to Unify Directed and Undirected Graphical Models (2002) (86)
- Mixtures of local linear subspaces for face recognition (1998) (84)
- Signal-space characterization of iterative decoding (2001) (84)
- Variational Learning in Nonlinear Gaussian Belief Networks (1999) (83)
- Very loopy belief propagation for unwrapping phase images (2001) (79)
- Response to Comment on "Clustering by Passing Messages Between Data Points" (2008) (76)
- Time-series classification using mixed-state dynamic Bayesian networks (1999) (76)
- Inferring global levels of alternative splicing isoforms using a generative model of microarray data (2006) (70)
- Correction of a splicing defect in a mouse model of congenital muscular dystrophy type 1A using a homology-directed-repair-independent mechanism (2017) (70)
- Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes (2007) (68)
- Learning Wake-Sleep Recurrent Attention Models (2015) (65)
- Solving the Uncapacitated Facility Location Problem Using Message Passing Algorithms (2010) (64)
- Semi-Supervised Affinity Propagation with Instance-Level Constraints (2009) (63)
- Does the Wake-sleep Algorithm Produce Good Density Estimators? (1995) (63)
- Learning appearance and transparency manifolds of occluded objects in layers (2003) (62)
- Enforcing integrability for surface reconstruction algorithms using belief propagation in graphical models (2001) (61)
- Unsupervised image translation (2003) (61)
- Combination of statistical and rule-based approaches for spoken language understanding (2002) (61)
- Transformed hidden Markov models: estimating mixture models of images and inferring spatial transformations in video sequences (2000) (59)
- Fast Exact Inference for Recursive Cardinality Models (2012) (59)
- Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data (2012) (59)
- Unwrapping of MR phase images using a Markov random field model (2006) (56)
- Interactive Decoding of a Broadcast Message (2003) (54)
- Constructing Treatment Portfolios Using Affinity Propagation (2008) (54)
- Probabilistic Sparse Matrix Factorization (2004) (53)
- Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs (2005) (51)
- A probabilistic framework for embedded face and facial expression recognition (1999) (51)
- Detection and tracking of faces and facial features (1999) (48)
- Early Detection and Trellis Splicing: Reduced-Complexity Iterative Decoding (1998) (46)
- Introduction to the special issue on codes on graphs and iterative algorithms (2001) (45)
- Accounting for uncertainity in observations: A new paradigm for Robust Automatic Speech Recognition (2002) (43)
- Probability Propagation and Iterative Decoding (1996) (42)
- Computer vision for high content screening (2016) (42)
- Efficient variable length channel coding for unknown DMCs (2004) (42)
- Bayesian networks for pattern classification, data compression, and channel coding (1997) (42)
- Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome (2015) (41)
- Detecting MicroRNA Targets by Linking Sequence, MicroRNA and Gene Expression Data (2006) (40)
- Comparing Sequence and Expression for Predicting microRNA Targets Using GenMIR3 (2007) (40)
- Continuous Sigmoidal Belief Networks Trained using Slice Sampling (1996) (40)
- Probabilistic Inference of Speech Signals from Phaseless Spectrograms (2003) (39)
- AVISPA: a web tool for the prediction and analysis of alternative splicing (2013) (39)
- Fast, Large-Scale Transformation-Invariant Clustering (2001) (37)
- Cumulative Distribution Networks and the Derivative-sum-product Algorithm: Models and Inference for Cumulative Distribution Functions on Graphs (2008) (36)
- Learning Graphical Models of Images, Videos and Their Spatial Transformations (2000) (36)
- A generalizable pre-clinical research approach for orphan disease therapy (2012) (36)
- Transformation-Invariant Clustering and Dimensionality Reduction Using EM (2001) (35)
- COSSMO: predicting competitive alternative splice site selection using deep learning (2018) (34)
- ALGONQUIN - Learning Dynamic Noise Models From Noisy Speech for Robust Speech Recognition (2001) (33)
- Sequentially Fitting "Inclusive" Trees for Inference in Noisy-OR Networks (2000) (32)
- Learning Dynamic Noise Models from Noisy Speech for Robust Speech Recognition (2001) (31)
- A Winner-Take-All Method for Training Sparse Convolutional Autoencoders (2014) (31)
- Information for : “ C 2 H 2 zinc finger proteins greatly expand the human regulatory lexicon ” (2014) (31)
- Inference of the human polyadenylation code (2017) (29)
- Speech recognition in adverse environments: a probabilistic approach (2002) (29)
- Generative Model for Layers of Appearance and Deformation (2005) (28)
- Event-coupled hidden Markov models (2000) (27)
- Species The Evolutionary Landscape of Alternative Splicing in Vertebrate (2013) (27)
- Using ``epitomes'' to model genetic diversity: Rational design of HIV vaccine cocktails (2005) (26)
- Network cleanup (2013) (24)
- Model-based detection of alternative splicing signals (2010) (24)
- Structured ranking learning using cumulative distribution networks (2008) (24)
- Flexible Priors for Exemplar-based Clustering (2008) (24)
- Efficient Stochastic Source Coding and an Application to a Bayesian Network Source Model (1997) (23)
- Unwrapping phase images by propagating probabilities across graphs (2001) (22)
- A simple algorithm that discovers efficient perceptual codes (1997) (21)
- Graph Cuts is a Max-Product Algorithm (2011) (21)
- Filling in scenes by propagating probabilities through layers and into appearance models (2000) (21)
- ACCOUNTING FOR UNCERTAINTY IN OBSERVATIONS : A NEW PARADIGM FOR ROBUST AUTOMATIC SPEECH RECOGNITION (21)
- Advances in Algorithms for Inference and Learning in Complex Probability Models (2003) (20)
- GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data (2005) (20)
- Convolutional Factor Graphs as Probabilistic Models (2004) (20)
- Towards non-stationary model-based noise adaptation for large vocabulary speech recognition (2001) (20)
- Denoising and Untangling Graphs Using Degree Priors (2003) (20)
- Multibaseline InSAR terrain elevation estimation: a dynamic programming approach (2003) (20)
- Rateless Coding for Arbitrary Channel Mixtures With Decoder Channel State Information (2009) (19)
- Variational Learning in Mixed-State Dynamic Graphical Models (1999) (19)
- Free energy coding (1996) (18)
- Topographic Transformation as a Discrete Latent Variable (1999) (18)
- cDeepbind: A context sensitive deep learning model of RNA-protein binding (2018) (17)
- A Segmental HMM for Speech Waveforms (2004) (17)
- Embedded face and facial expression recognition (1999) (17)
- Does conservation account for splicing patterns? (2016) (16)
- Local Probability Propagation for Factor Analysis (1999) (15)
- A segment based probabilistic generative model of speech (2005) (15)
- Allele-specific transcription factor binding as a benchmark for assessing variant impact predictors (2018) (15)
- Addendum: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing (2009) (15)
- Probabilistic n-Choose-k Models for Classification and Ranking (2012) (15)
- Computational refinement of post-translational modifications predicted from tandem mass spectrometry (2011) (14)
- Turbo Factor Analysis (1999) (14)
- Probabilistic Inference in Graphical Models (1998) (14)
- Rateless Coding for Non-Ergodic Channels with Decoder Channel State Information (2006) (13)
- Separating appearance from deformation (2001) (12)
- Fast Transformation-Invariant Component Analysis (2008) (12)
- Matrix Tile Analysis (2006) (11)
- Variational Probabilistic Speech Separation Using Microphone Arrays (2007) (11)
- Fast Transformation-Invariant Factor Analysis (2002) (9)
- Concurrent turbo-decoding (1997) (9)
- Learning Montages of Transformed Latent Images as Representations of Objects That Change in Appearance (2002) (9)
- Robust variational speech separation using fewer microphones than speakers (2003) (9)
- Transcriptional Profiling of Endocrine Cerebro-Osteodysplasia Using Microarray and Next-Generation Sequencing (2011) (9)
- Spatial Bias Removal in Microarray Images (2003) (9)
- On interacting encoders and decoders in multiuser settings (2004) (9)
- GenRate: A Generative Model That Finds and Scores New Genes and Exons in Genomic Microarray Data (2004) (8)
- Min-Max Problems on Factor Graphs (2014) (8)
- Survey Propagation beyond Constraint Satisfaction Problems (2016) (8)
- Learning Generative Models of Similarity Matrices (2002) (8)
- Learning to cluster using local neighborhood structure (2004) (8)
- Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry (2013) (8)
- Learning in Biomedicine and Bioinformatics Using Affinity Propagation (2007) (7)
- Learning structural element patch models with hierarchical palettes (2012) (7)
- How Many New Genes Are There? (2006) (7)
- Learning the "Epitome" of an Image (2002) (7)
- An iterative dynamic programming approach to 2-D phase unwrapping (2002) (7)
- Robust variational speech separation using fewer microphones than speakers (2003) (7)
- HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps (2020) (7)
- Real-time On-line Learning of Transformed Hidden Markov Models from Video (2003) (7)
- The automated extraction of environmentally relevant features from digital imagery using Bayesian multi-resolution analysis (2001) (6)
- Variational Speech Separation of More Sources than Mixtures (2005) (6)
- Probabilistic estimation of short sequence expression using RNA-Seq data and the “positional bootstrap” (2016) (6)
- Learning better image representations using ‘flobject analysis’ (2011) (6)
- Finding Novel Transcripts in High-Resolution Genome-Wide Microarray Data Using the GenRate Model (2005) (6)
- Cross-Pollination in Signal Processing Technical Areas (2009) (6)
- Accumulator Networks: Suitors of Local Probability Propagation (2000) (6)
- A Bayesian Model That Links Microarray mRNA Measurements to Mass Spectrometry Protein Measurements (2007) (5)
- ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping (2019) (5)
- Using epitomes to model genetic diversity: Rational design of HIV vaccines (2005) (5)
- GenRate: A Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data (2006) (4)
- Min-Max Propagation (2017) (4)
- Noise robust speech recognition using Gaussian basis functions for non-linear likelihood function approximation (2002) (4)
- A Generative Model of Dense Optical Flow in Layers (2004) (4)
- "Codes" on images and iterative phase unwrapping (2001) (4)
- Interpreting Graph Cuts as a Max-Product Algorithm (2011) (4)
- Unwrapping phases by relaxed mean field inference (2001) (3)
- Bayesian Learning of MicroRNA Targets from Sequence and Expression Data (2006) (3)
- Product Analysis: Learning to Model Observations as Products of Hidden Variables (2001) (3)
- nonsense-mediated mRNA decay to control gene expression widespread coupling of alternative splicing with Quantitative microarray profiling provides evidence against Material Supplemental (2006) (3)
- Embracing a New Golden Age of Signal Processing (2009) (3)
- ATP7B variant c.1934T > G p.Met645Arg causes Wilson disease by promoting exon 6 skipping. (2020) (3)
- Markovian inference in belief networks (1998) (3)
- Training Restricted Boltzmann Machine by Perturbation (2014) (3)
- A Factorized Variational Technique for Phase Unwrapping in Markov Random Field (2001) (2)
- Iterative analysis of microarray data (2004) (2)
- Factor Analysis Using Batch and Online EM (1999) (2)
- Analysis of an iterative dynamic programming approach to 2-D phase unwrapping (2002) (2)
- Code and wavelet excited linear prediction of speech (1993) (2)
- Joint Design of Data Analysis Algorithms and User Interfaces for Video Applications (2003) (2)
- Probabilistic Inference of Alternative Splicing Events in Microarray Data (2004) (2)
- Iterated Conditional Modes for Cross-Hybridization Compensation in DNA Microarray Data (2004) (1)
- MBNL proteins repress embryonic stem cell-specific alternative splicing and reprogramming (2014) (1)
- Nonparametric Bayesian Approach to Post-translational Modification Refinement of Predictions from Tandem Mass Spectrometry (2012) (1)
- Phase unwrapping by minimizing Kikuchi free energy (2002) (1)
- RTfold: RNA secondary structure prediction using deep learning with domain inductive bias (2022) (1)
- Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data (2012) (1)
- Inferring Alternative Splicing Combinations from Comprehensive Putative-Junction Microarray Data (2008) (1)
- Probabilistic sparse matrix factorization with an application to discovering gene functions in mouse mRNA expression data (2004) (1)
- Learning mixtures of smooth, nonuniform deformation models for probabilistic image matching (2001) (1)
- A graph neural network approach for molecule carcinogenicity prediction (2021) (1)
- Keeping Flexible Active Contours on Track using Metropolis Updates (2000) (1)
- Carninci The Transcriptional Landscape of the Mammalian Genome (2011) (1)
- AVISPA: a web tool for the prediction and analysis of alternative splicing (2013) (1)
- Curiosity in Science and Technology (2009) (1)
- Shining Bright: The Golden Era of Signal Processing (2011) (1)
- Factorgrams: A tool for visualizing multi-way associations in biological data (2006) (1)
- A Computational High-Throughput Method for Detecting miRNA Targets (2005) (1)
- Machine Learning Approaches for RNA Editing Prediction (2020) (0)
- Additional file 3 of Does conservation account for splicing patterns (2016) (0)
- January 20 , 2004 UTML TR 2004 – 001 A Segmental HMM for Speech Waveforms (2004) (0)
- Early Detection and Trellis Splicing Reduced Complexity Soft Iterative Decoding (1998) (0)
- Impacto Global da Signal Processing Magazine (2011) (0)
- Manuscript Word Count: Abstract: 193; Text, with citations, without references: 3921 Number of Tables: 2; Supplemental Files: Yes Whole-genome sequencing suggests schizophrenia risk mechanisms in humans with 22q11.2 deletion syndrome (2015) (0)
- IMA Seminar Series 2008 / 2009 (2009) (0)
- Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass (2013) (0)
- Perspectives on Special Issues (2009) (0)
- Transformation-Invariant Clustering and Linear Component Analysis using the EM Algorithm (2016) (0)
- Additional file 2 of Does conservation account for splicing patterns (2016) (0)
- New Honor, New Initiatives, and New Impact to Come (2011) (0)
- STORMSeq: A Method for Ranking Regulatory Sequences by Integrating Experimental Datasets with Diverse Computational Predictions (2011) (0)
- A Robust and Efficient Method to Unwrap MR Phase Images (2002) (0)
- Comparison of GenASAP with supervised methods (2005) (0)
- Bayesian Belief Networks (2006) (0)
- Variational inference for continuous sigmoidal Bayesian networks (1996) (0)
- Bayesian n-Choose-k Models for Classification and Ranking (2012) (0)
- Embedded Fa e and Fa ial Expression Re ognitionAntonio (1999) (0)
- Learning Better Image Representations Using ‘ Flobject Analysis ’ : Supplementary Material (2011) (0)
- A Phenomic assessment of sub-cellular morphology in S. cerevisiae using synthetic genetic array and high-content screening (2015) (0)
- A comparison of Gibbs , Bethe , and Kikuchi free energies using Monte Carlo simulations (0)
- Impact of Signal Processing and of Our Work (2010) (0)
- Bayesian Painting by Numbers: Flexible Priors for Colour-Invariant Object Recognition (2013) (0)
- Points Clustering by Passing Messages Between Data (2007) (0)
- Balancing rewrapping error and smoothness in two dimensional phase unwrapping problems (2002) (0)
- collagen and mechanical forces Biomechanics of the lung parenchyma: critical roles of (2005) (0)
- Hierarchical Affinity Propagation Supplementary Material (2011) (0)
- Factorizing appearance using epitomic flobject analysis (2012) (0)
- Beyond genomics: Detecting codes and signals in the cellular transcriptome [Plenary speakers] (2006) (0)
- Messages Between Data Points " Response to Comment on " Clustering by Passing (2008) (0)
- Learning mixtures of smooth , nonuniformdeformation models for probabilisti image mat (2007) (0)
- List of Tissue Specific Critical Exons (2014) (0)
- Translating images by unsupervised estimation of switching filters (2004) (0)
- Future Research Directions (1998) (0)
- Does conservation account for splicing patterns? (2016) (0)
- transcriptomes Widespread intron retention in mammals functionally tunes Material (2014) (0)
- Genome analysis Inference of the human polyadenylation code (2018) (0)
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