PropertyDAG: Multi-objective Bayesian optimization of partially ordered, mixed-variable properties for biological sequence design

no code implementations • 8 Oct 2022 • Ji Won Park, Samuel Stanton, Saeed Saremi, Andrew Watkins, Henri Dwyer, Vladimir Gligorijevic, Richard Bonneau, Stephen Ra, Kyunghyun Cho

Bayesian optimization offers a sample-efficient framework for navigating the exploration-exploitation trade-off in the vast design space of biological sequences.

Active Learning

Multi-segment preserving sampling for deep manifold sampler

no code implementations • 9 May 2022 • Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew Watkins, Vladimir Gligorijević, Richard Bonneau, Stephen Ra, Kyunghyun Cho

We introduce an alternative approach to this guided sampling procedure, multi-segment preserving sampling, that enables the direct inclusion of domain-specific knowledge by designating preserved and non-preserved segments along the input sequence, thereby restricting variation to only select regions.

Language Modelling