Batched Energy-Entropy acquisition for Bayesian Optimization

Bayesian optimization (BO) is an attractive machine learning framework for performing sample-efficient global optimization of black-box functions. The optimization process is guided by an acquisition function that selects points to acquire in each round of BO. In batched BO, when multiple points are acquired in parallel, commonly used acquisition functions are often high-dimensional and intractable, leading to the use of sampling-based alternatives. We propose a statistical physics inspired acquisition function for BO with Gaussian processes that can natively handle batches. Batched Energy-Entropy acquisition for BO (BEEBO) enables tight control of the explore-exploit trade-off of the optimization process and generalizes to heteroskedastic black-box problems. We demonstrate the applicability of BEEBO on a range of problems, showing competitive performance to existing methods.

BEND: Benchmarking DNA Language Models on biologically meaningful tasks

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.