4 papers
Direct RNA sequence design under codon constraints using expressive tensor-based secondary structure models
Mark Fornace, Christina Wuyan Wang, Michael Lindsey
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein,…
Linear Systems and Eigenvalue Problems: Open Questions from a Simons Workshop
Noah Amsel, Yves Baumann, Paul Beckman +36
This document presents a series of open questions arising in matrix computations, i.e., the numerical solution of linear algebra problems. It is a result of working groups at the w…
An approximation theory for Markov chain compression
Mark Fornace, Michael Lindsey
We develop a framework for the compression of reversible Markov chains with rigorous error control. Given a subset of selected states, we construct reduced dynamics that can be lif…
Column and row subset selection using nuclear scores: algorithms and theory for Nyström approximation, CUR decomposition, and graph Laplacian reduction
Mark Fornace, Michael Lindsey
Column selection is an essential tool for structure-preserving low-rank approximation, with wide-ranging applications across many fields, such as data science, machine learning, an…