Colloquium D. Gusfield – Mardi 17 novembre 2020

Le mardi 17 novembre 2020 à 15h30 a eu lieu notre colloquium, en visioconférence.

Nous avons eu le plaisir d’écouter Dan Gusfield, professeur émérite du département informatique à l’Université Davis de Californie.

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Integer Linear Programming in Computational and Systems Biology

Abstract: Integer linear programming is increasingly being used in computational biology in non-traditional ways: to model biological phenomena, to analyze biological data, and to extract biological insight from the models and the data. Best-of-breed ILP solvers have proven to be effective in tackling problem instances of importance in biology, thereby opening huge opportunities in this area. However, there are challenges in effectively using these tools for biological problems.
In this talk, we explore the use of integer programming in computational biology and explain how it differs from traditional uses of integer programming. This will be illustrated through the particular problem of predicting the two-dimensional folding of RNA molecules. It’s important to note that attendees are not required to have a biological background – as all key concepts will be introduced and explained during the talk.
In the talk, we discuss: The basic model and problem of RNA folding, and how it is implemented and solved as an integer linear program.
Simple biological extensions of the basic RNA folding model and how they are modeled and solved using integer linear programming.
Two challenging extensions of the model, base-stacking and pseudo-knots, and how these are modeled and solved using integer linear programming.
If time allows, we will also mention efforts to solve RNA folding problems, and other biological problems, using SAT-solving instead of integer programming.

Short Bio: Dan Gusfield is Distinguished Professor Emeritus in the department of computer science at the University of California, Davis. He is a fellow of the IEEE, the ACM, and the International Society of Computational Biology, as well as the author of the recently published book “Integer Linear Programming in Computational and Systems Biology: An entry-level text and course”, published by Cambridge University Press. The RNA folding problems that will be discussed in this talk are covered in one of the chapters in the book.