革新知能統合研究センター

Speaker:
Ritu Kundu (King’s College London)

Personal homepage:
https://nms.kcl.ac.uk/ritu.kundu/index.html

Title:
Superbubbles and Elastic-Degenerate Strings: Towards better representations of a cohort of sequences

Abstract:
In many application domains dealing with sequential data, it becomes advantageous to organise multiple distinct-but-similar sequences as a single entity. For example, in human genomics, the reference genome has been represented as a single sequence so far but with the availability of a vast collection of human genomes, so called reference cohorts seem more sensible in order to avoid the reference-bias presented by a single genomic sequence. Different representations have recently been explored in an attempt to organise human genomic sequences (which are highly similar) in reference cohorts. Each such representation has its own challenges. This talk describes solutions to two such challenges in two different representations. Specifically, the talk will be about finding “Superbubbles” (special self-contained subgraphs) in a graphical model and pattern-matching in “Elastic-Degenerate Strings” (sequences with positions where multiple varying length subsequences can occur).