Invited talk: Automata processor and its applications in bioinformatics

Summary form only given. This talk will introduce the Micron Automata Processor, a novel computing architecture that permits massively parallel execution of multiple non-deterministic finite automata. The Automata Processor inspires a new programming paradigm of solving problems using complex pattern matching engines executed over streaming data. The first part of this talk will focus on the processor characteristics, programming and execution environment, and some general algorithm design principles we discovered that are of value in designing applications on the Automata Processor. In the second part, I will describe ongoing work in my research group on solving bioinformatics applications using the Automata Processor. In particular, I will describe a solution to the NP-hard problem of finding motifs in biological sequences. Our solution uses a single Automata Processor board to tackle problem instances much larger than what is reported in the literature so far.