PeopleofSuperintelligence

Researcher

Brendan Frey

Brendan Frey is a machine-learning researcher whose work connects deep learning with genome biology. He worked with Geoffrey Hinton on the wake-sleep algorithm in 1995, completed a PhD at the University of Toronto in 1997, and joined its engineering department in 2001. His research includes affinity propagation and a machine-learning splicing code; he helped develop DeepBind, which studies DNA- and RNA-binding proteins, and co-founded Deep Genomics in 2015. As of October 2026, he is Chief Innovation Officer and co-founder of Deep Genomics and a professor at Toronto.

Now at
University of Toronto, Deep Genomics and Vector Institute
Works
266
Citations
43,497
h-index
69
Badges

Publication numbers from OpenAlex, as of 19 October 2026.

Timeline

  1. 1995–2001

    The wake-sleep algorithm

    In 1995, he and Geoffrey Hinton work on the wake-sleep algorithm, which helps launch deep learning. He completes a PhD under Hinton at the University of Toronto in 1997. In 2001, he joins Toronto's Electrical and Computer Engineering department.

  2. 2007–2010

    Affinity propagation and splicing

    In 2007, his work includes affinity propagation, an algorithm published in Science. In 2010, his research includes inference of genetic codes governing gene expression and alternative splicing. With Benjamin Blencowe's team, he uses machine learning to analyze splicing rules together.

  3. 2011

    A Polanyi Award

    Frey and Benjamin Blencowe receive the 2011 NSERC John C. Polanyi Award for work on a gene-regulatory code and a machine-learning framework for analyzing splicing rules.

  4. 2015

    Founding Deep Genomics

    In 2015, he co-founds Deep Genomics, a startup that applies artificial intelligence to decode the effects of genetic mutations and identify therapeutic targets.

  5. 2016

    DeepBind wins Invention of the Year

    He and co-inventors Babak Alipanahi and Andrew Delong receive the University of Toronto's Invention of the Year Award for DeepBind, a deep-learning application that identifies the specificities of DNA- and RNA-binding proteins.

  6. 2020

    CEO and Vector founding member

    In 2020, he is CEO of Deep Genomics and a founding member of the Vector Institute for Artificial Intelligence.

  7. As of October 2026

    Chief Innovation Officer

    As of October 2026, he is Chief Innovation Officer and co-founder of Deep Genomics and a professor of Engineering and Medicine at the University of Toronto. His research group develops machine-learning algorithms and studies genome biology. In August 2026, he writes about AI for genetic medicine on the company blog.

Career

  1. Since 2015Deep GenomicsCo-founder, CEO
  2. Since 2001University of TorontoProfessor of Engineering and Medicine
  3. 2020–2026Vector InstituteFounding Member
  4. 2014–2015CIFAR
  5. 1999–2001University of Waterloo
  6. 1997–2001University of Illinois Urbana-Champaign

Education

  1. 1997University of TorontoPhD

From the biography and OpenAlex affiliations (the years of papers that list the organization), so some years are approximate.

Most-cited works

  1. Clustering by Passing Messages Between Data Points2007 · Science · 6,764 citations
  2. Factor graphs and the sum-product algorithm2001 · IEEE Transactions on Information Theory · 6,475 citations
  3. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing2008 · Nature Genetics · 3,941 citations
  4. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning2015 · Nature Biotechnology · 2,862 citations
  5. Adversarial Autoencoders2015 · 1,521 citationsWith Ian Goodfellow

From OpenAlex, as of 19 October 2026.

  1. 14% of AI doctorate holders from 2010 to 2016 founded or led a company or lab by 10 years after graduationIncludes Brendan Frey. We estimate how often AI doctorate holders founded or led a company or lab by 10 years after their doctorate, and how the timing changed across cohorts.
  2. Stanford University trained or employed 26 of the 108 AI major-prize winners, more than any other universityIncludes University of Toronto. Stanford University trained or employed 26 of the 108 AI major-prize winners, more than any other university. We compare doctorate and employment links for major-prize and best-paper winners.
  3. More people shaping AI studied at Massachusetts Institute of Technology than at any other institutionIncludes University of Toronto. Our estimates of where the people shaping AI studied and where their careers led, from education records in cited biographies.
  4. 44% of AI career moves go from one university to anotherIncludes University of Toronto. We estimate how 13,335 AI career moves link universities, companies, labs and government research centers, with net flows and the most common paths.

Colleagues

People named in this biography, and people with dated positions at the same organization in the same years.

Sources and credits

Photo: We have no published photo of Brendan Frey yet. Send us a free-licensed photo.

  1. Team | Deep Genomics deepgenomics.com. Checked 18 October 2026.
  2. Six degrees of separation: how U of T's Geoffrey Hinton is connected to top AI researchers around the world utoronto.ca. Checked 18 October 2026.
  3. Brendan Frey en.wikipedia.org. Checked 18 October 2026.
  4. Frey, Brendan Professor - Electrical & Computer Engineering ece.utoronto.ca. Checked 18 October 2026.
  5. Visual Culture | University of Toronto utoronto.ca. Checked 18 October 2026.
  6. Brendan Frey wins Invention of the Year award ece.utoronto.ca. Checked 18 October 2026.
  7. U of T’s Deep Genomics secures $40 million in financing for AI drug development platform: Betakit utoronto.ca. Checked 18 October 2026.
  8. AI and Genetic Medicine Need Each Other deepgenomics.com. Checked 18 October 2026.