University Research Services

University Research Services
University Research Services

Fields Day @ Queen's on November 19, 2019

10:30 am to 3:00 pm in BioSciences 1102 (presentations) and BioSciences atrium (lunch and networking)

RSVPs are required by November 8: Registration form Seating for lunch and the networking sessions is limited and will be allocated on a first come first serve basis.  

Event Description: The goal of this event is to familiarize faculty members across Queen's with the programs of the Fields Institute, and to facilitate new interdisciplinary collaborations related to mathematics across campus. Queen's is one of nine sponsoring universities of the Fields Institute for Research in the Mathematical Sciences. The Institute promotes mathematical activity in Canada and the collaboration between mathematicians and those working in other disciplines such as engineering, the physical and biological sciences, medicine, economics, finance, telecommunications and information systems.

Fields Day at Queen's will include an overview of Fields Institute programs, a public lecture by Dr. Lila Kari, and two interdisciplinary networking sessions for faculty members:

Schedule

Dr. Ted Hsu will be the MC of the morning portion of the event. 

10:30-10:45 am: BioSci 1102: Land acknowledgement and welcomes by Queen's OVPR and Fields Institute

10:45-11:15 am : BioSci 1102: Fields Institute programs, presented by Drs. James Mingo and Kim McAuley

11:15pm-12:15 pm: BioSci 1102: Public lecture by Dr. Lila Kari "Machine Learning and the Mathematics of Genomes"

12:15 pm – 1:15 pm: BioSci atrium: Networking lunch for professors

1:15-2:45pm: BioSci atrium: Structured networking session for professors, including a short presentation by Dr. Martin Guay. 

2:45 pm Concluding remarks


RSVPs are required by November 8: Registration form Seating for lunch and the networking sessions is limited and will be allocated on a first come first serve basis.

Event contact for questions: Vera Kettnaker, vmk@queensu.ca, 613-533-6000 x77314

Organizing committee:  Stéphane Courteau, Vera Kettnaker, Xiang Li and Serdar Yuksel. 


Presentation abstract: 

Machine Learning and the Mathematics of Genomes

In the same way we use the twenty-six letters of the alphabet to write text, and the two bits 0 and 1 to write computer code, the four basic DNA units (Adenine, Cytosine, Guanine, Thymine) are used by Nature to encode information as DNA strands. Theoretically, a DNA strand can be viewed as a "word" over the four-letter alphabet {A; C; G; T}, and the mathematical structure of such words has implications for their biological structure and function. This talk describes our research into the mathematical properties of genomic DNA sequences by exploring the connection between word frequencies in a genome and the type of organism that the genome belongs to. In particular, I describe our investigation into the Chaos Game Representation of a DNA sequence as a potential "genomic signature" of its species. Moreover, I describe how we combine supervised machine learning techniques with such genomic signatures for ultrafast, accurate, and scalable algorithms for species identification and classification. The potential impact of such alignment-free universal classification algorithms could be significant, given that 86% of existing species on Earth and 91% of species in the oceans still await classification.

Speaker Biography:

Lila Kari is Professor and University Research Chair in the School of Computer Science at the University of Waterloo, where she moved from her previous position in the Department of Computer Science at the University of Western Ontario (1993-2017). She received her M.Sc. in 1987 from the University of Bucharest, Romania, and her Ph.D. in 1991 for her thesis "On Insertions and Deletions in Formal Languages", for which she received the Rolf Nevanlinna doctoral thesis award for the best doctoral thesis in mathematics in Finland. Author of more than 200 peer reviewed articles, Professor Kari is regarded as one of the world's experts in the area of biomolecular computation, that is using biological, chemical and other natural systems to perform computations. In 2015 she received the Rozenberg Tulip Award for the DNA Computer Scientist of the Year, awarded at the 21st International conference on DNA Computing and Molecular Programming, Harvard University, USA , for her contributions in advancing formal theoretical models and exemplary leadership in the field. The award is presented by the International Society for Nanoscale Science, Computation and Engineering , ISNSCE, annually and recognizes a prominent scientist who has shown continuous contributions, pioneering, original contributions, and who has influenced the development of the field.

She is Editor-in-Chief of the journal Theoretical Computer Science-C (theory of natural computing), as well as Editor-in-Chief of the Springer Natural Computing Book Series. She has served as Steering Committee Chair for the DNA Computing and Molecular Programming conference series, as Steering Committee member for the Unconventional Computation and Natural Computation conference series, as well as on the Scientific Advisory Committee of the International Society for Nanoscale Science, Computation, and Engineering. She has additionally served as a member of the Board of Directors of the FIELDS Institute for Research in Mathematical Sciences, the UK EPSRC Peer Review College, on the NSERC Grant Selection Committee on Computing and Information Systems, the NSERC Herzberg-Brockhouse-Polanyi Prize joint selection committee, and NSERC Steacie Memorial Fellowship committee. Her current research focuses on biodiversity informatics, as well as theoretical aspects of bioinformation and biocomputation, including models of cellular computation, nanocomputation by DNA self-assembly and Watson-Crick complementarity in formal languages.