Bonnie Berger

Efficient minimizer orders for large values of <i>k</i> using minimum decycling sets

2022 · bioRxiv (Cold Spring Harbor Laboratory)

Abstract Minimizers are ubiquitously used in data structures and algorithms for efficient searching, mapping, and indexing of high-throughput DNA sequencing data. Minimizer schemes select a minimum k -mer in every L -long sub-sequence of the …

Dirichlet Flow Matching with Applications to DNA Sequence Design

2024 · PubMed

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from …