Anđela Todorović

Information & Communications Technology

Machine Learning and AI Software Engineering

Niš, Central Serbia, Serbia

Gene genealogies reconstruction on large-scale BALSAC data

The objective of this talk arises from the reconstruction of gene genealogies problem - from a given genotypes of sequence data from contemporary individuals and an extended pedigree of genealogical relationships among them, we have to decide and be very clear about what we should consider to be nodes information in genealogy tree according to kinds of dependencies among these nodes which should be considered to be edges of the tree.

This talk will present novel algorithms for advanced reconstruction of
the gene genealogy by performing inference on graphical models, specifically, implementing greedy and belief propagation algorithms on the succinct tree sequences.The implemented algorithms will in turn be integrated into the existing tskit and msprime libraries. The succinct tree sequence is a recently introduced encoding for recombinant ancestry that takes advantage of the correlations between adjacent trees. Considering that tree sequence data structure has the potential to hugely reduce storage and processing costs, it is a natural (if not the only) contender to tackle this problem.


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