In 1993, Morgan and Herve Bourlard published their work on the hybrid system approach to
speech recognition, which uses neural networks probabilistically with Hidden Markov Models (HMMs). The system improved automatic speech recognition techniques based on HMMs by providing discriminative training, incorporating multiple input sources, and using a flexible architecture able to accommodate contextual inputs and feedbacks. The work has been described as "seminal.". Morgan won the 1996 IEEE Signal Processing Magazine Best Paper Award for a paper with Bourlard. Morgan and Bourlard were awarded the 2022
IEEE James L. Flanagan Speech and Audio Processing Award "For contributions to neural networks for statistical speech recognition." Morgan was the principal investigator of the
IARPA-funded project Outing Unfortunate Characteristics of HMMs, which sought to identify problems in automatic speech recognition technology. He also led a team of universities to build speech recognition systems for low resource languages as part of the IARPA
Babel program. Morgan was the former director of the
International Computer Science Institute (ICSI), where he was also the Speech Group leader. He recently has focused on campaign reform through empowering volunteerism. In that work, he co-founded UpRise Campaigns with Antonia Scatton, and later co-founded Neighbors Forward AZ with Alison Porter. As of 2023, he is the Chair of the Census and Redistricting Committee in the Arizona Democratic Party. Morgan has produced more than 200 publications, including four books, == Honors and awards ==