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The Theoretical Analysis of Sequencing Bioinformatic Algorithms

Series: Bangalore Theory Seminars

Speaker: Paul Medvedev, Pennsylvania State University

Date/Time: Jul 15 16:00:00

Location: Online (MS Teams link below)

Abstract:
The theoretical analysis of algorithm performance has been an important tool in the engineering of algorithms in many application domains. Its goals are to predict the empirical performance of an algorithm and to be a yardstick that drives the design of novel algorithms that perform well in practice. However, when it comes to sequencing bioinformatics, an application area concerned with algorithms for biological sequencing data, theoretically analyzing algorithms has been challenging has had a mixed record in achieving its goals.

In this talk, I will make an attempt at the first systematic and critical survey of the application of theoretical analysis of algorithm techniques to sequencing bioinformatics. I explore some of the techniques that have been applied and the extent to which they have been successful. I use the edit distance computation problem as a case study but also explore the problems of genome assembly, structural variation detection, and compact data structures. I conclude by discussing steps that can be taken to help improve the impact and applicability of the theoretical analysis of algorithms in sequencing bioinformatics.

The talk covers material from two recent survey papers: (i) Link and (ii) Link

Microsoft teams link: Link

We are grateful to the Kirani family (Link and the Walmart Center for Tech Excellence (Link for generously supporting this seminar series


Hosts: KVN Sreenivas, Rameesh Paul, Rahul Madhavan, Debajyoti Kar, Nirjhar Das