Ph.D. Defense by Ole Torp Lassen Nov 28th 2011
Ole Torp Lassen defends his thesis: Compositionality in probabilistic logic modelling for biological sequence analysis
Monday the 28th November 2011 at 13.00 – 16.00 in the auditorium of building 46
Abstract
Systems that combine logic programming and statistical inference allow machine-learning systems to deal with both relational and statistical information. Serious challenges with regard to efficiency of computation are however also integral to such systems. In the dissertation, I experiment with using one such system, PRISM (Taisuke Sato & Yoshitaka Kameya), for specifying probabilistic logic programs for in particular gene-finding in DNA. As part of the general domain of DNA-annotation, the task of gene-finding is characterized by large sets of extremely long and highly ambiguous sequences of data, and represents a challenging setting for efficient analysis. I present a compositional system, Bayesian Annotation Networks, where the complex overall task is optimized or approximated by identifying and negotiating interdependent constituent subtasks and, in turn, integrating their analytical results according to their inter-dependencies. I exemplify the methodology on two practical problems related to gene-finding and suggest directions for future work.
Assessment Committee
Troels Andreasen, Associate Professor, CBIT, Roskilde University (chairman)
Veronica Dahl, Professor, Simon Fraser University, Canada
Anders Krogh, Professor, Biology, University of Copenhagen
Head of the defense
Keld Bødker, Head of Doctoral School, CBIT, Roskilde University
Supervisor
Henning Christiansen, Professor, CBIT, Roskilde University
Thesis is available for examination at Roskilde University Library.
After the defense CBIT will host a reception