Born and raised in Europe, he received his Ph.D. in Mathematics from the California Institute of Technology in 1986. From 1986 to 1988, he was a postdoctoral fellow at the University of California, San Diego. From 1988 to 1995, he held faculty and member of the technical staff positions at the California Institute of Technology and at the Jet Propulsion Laboratory (where he was given the Lew Allen Award for Research Excellence in 1993). He was CEO of a start up company called Net-ID from 1995 to 1999 and joined UCI in 1999.
Baldi is a Fellow of the Association for the Advancement of Artificial Intelligence and the American Association for the Advancement of Science.
Baldi's research include machine learning, artificial intelligence and large-scale data analysis, understanding and predicting protein structures, computational screening, systems biology, genome evolution, mining large software repositories, and communication networks.
Pierre Baldi has over 250 publications in his field of research and four books and many of them are highly cited.