Brendan John Frey FRSC (born 29 August 1968) is a Canadian-born machine learning and genome biology researcher, known mainly for his work on factor graphs, the wake-sleep algorithm for deep learning, and using machine learning to model genome biology and understand genetic disorders. He founded Deep Genomics and is currently its CEO, and he is a Professor of Engineering and Medicine at the University of Toronto. He co-developed a new computational approach to identifying the genetic determinants of disease, was one of the first researchers to successfully train a deep neural network, and was a pioneer in the introduction of iterative message-passing algorithms.

Frey studied computer engineering and physics at the University of Calgary (BSc 1990) and the University of Manitoba (MSc 1993), and then studied neural networks and graphical models as a doctoral candidate at the University of Toronto under the supervision of Geoffrey Hinton (PhD 1997). He was an invited participant of the Machine Learning program at the Isaac Newton Institute for Mathematical Sciences in Cambridge, UK (1997) and was a Beckman Fellow at the University of Illinois at Urbana Champaign (1999).

Following his undergraduate studies, Frey worked as a Junior Research Scientist at Bell-Northern Research from 1990 to 1991. After completing his postdoctoral studies at the University of Illinois at Urbana-Champaign, Frey was an Assistant Professor in the Department of Computer Science at the University of Waterloo, from 1999 to 2001.

In 2001, Frey joined the Department of Electrical and Computer Engineering at the University of Toronto and was cross-appointed to the Department of Computer Science, the Banting and Best Department of Medical Research and the Terrence Donnelly Centre for Cellular and Biomolecular Research. From 2008 to 2009, he was a Visiting Researcher at Microsoft Research, Cambridge, UK, and a Visiting Professor in the Cavendish Laboratories and Darwin College at Cambridge University. Between 2001 and 2014, Frey consulted for several groups at Microsoft Research and acted as a member of its Technical Advisory Board.