Guest: Associate Prof. Arzucan Özgür, Boğaziçi Üniversitesi

Title: Language processing: From Natural to Molecular Languages

Date: December 13, 2023, 13.40-14.30

LocationFENS G032

Abstract: We can represent different types of data in the field of life sciences using text-based representations. In addition to texts such as scientific publications written in natural language, we can also represent molecules in text form and consider them as expressed in a specific molecular language. For example, we can represent DNA as a text written with an alphabet of four letters, each letter corresponding to a nucleotide, proteins as texts written with an alphabet of 20 letters, each letter corresponding to an amino acid, and chemical compounds as texts written with the letters of their atoms. Processing and understanding these molecular languages, in addition to the millions of articles written in natural language, will enable a better understanding of life and health and shed light on the development of novel prevention, diagnosis and treatment strategies for diseases. In this talk, I will summarize the recent studies we have conducted on the automatic extraction of information from scientific articles using natural language processing techniques as well as the discovery of interactions between molecules using molecular language processing approaches.

Bio: Arzucan Özgür is a faculty member at the Computer Engineering Department of Boğaziçi University and co-director of the Text Analytics and Bioinformatics (TABI) Lab. She received her PhD in computer science and engineering from the University of Michigan in 2010. She holds a MS and a BS degree in computer engineering from Boğaziçi University. Her research interests include natural language processing and bioinformatics. Her recent focus has been on developing methods for processing and understanding textual data in natural (human) languages or in the sequences of biomolecules. Dr. Özgür is a recipient of the Science Academy Young Scientist Award (BAGEP 2016) and Turkish Science Academy Outstanding Your Scientist Award (TÜBA-GEBİP 2019). Her work has been supported by the Scientific and Technological Research Council of Türkiye (TÜBİTAK), European Commission Marie Curie CIG, and European Research Council (ERC).