LLL’05 Challenge: Genic Interaction Extraction - Identification of Language Patterns Based on Alignment and Finite State Automata

We present a system for the identification of syntax patterns describing interactions between genes and proteins in scientific text. The system uses sequence alignments applied to sentences annotated with interactions and syntactical information (part-of-speech), as well as finite state automata optimized with a genetic algorithm. Both methods identified syntactical patterns that are generalizations of textual representations of agenttarget relations. We match the generated patterns against arbitrary text to extract interactions and their respective partners. Our best system uses finite state automata optimized with a genetic algorithm, and scored an F1-measure of 51.8% on the LLL’05 evaluation set.