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Optimizing discrete black-box functions is key in several domains, e.g. protein engineering and drug design. Due to the lack of gradient information and the need for sample efficiency, Bayesian optimization is an ideal candidate for these tasks. Several methods for high-dimensional continuous and categorical Bayesian optimization have been proposed recently. However, our survey of the field reveals highly heterogeneous experimental set-ups across methods and technical barriers for the replicability and application of published algorithms to real-world tasks. To address these issues, we develop a unified framework to test a vast array of high-dimensional Bayesian optimization methods and a collection of standardized black-box functions representing real-world application domains in chemistry and biology. These two components of the benchmark are each supported by flexible, scalable, and easily extendable software libraries (poli and poli-baselines), allowing practitioners to readily incorporate new optimization objectives or discrete optimizers. Project website: https://machinelearninglifescience.github.io/hdbo_benchmark, Comment: Accepted at the Datasets and Benchmarks track of NeurIPS 2024

To optimize efficiently over discrete data and with only few available target observations is a challenge in Bayesian optimization. We propose a continuous relaxation of the objective function and show that inference and optimization can be computationally tractable. We consider in particular the optimization domain where very few observations and strict budgets exist; motivated by optimizing protein sequences for expensive to evaluate bio-chemical properties. The advantages of our approach are two-fold: the problem is treated in the continuous setting, and available prior knowledge over sequences can be incorporated directly. More specifically, we utilize available and learned distributions over the problem domain for a weighting of the Hellinger distance which yields a covariance function. We show that the resulting acquisition function can be optimized with both continuous or discrete optimization algorithms and empirically assess our method on two bio-chemical sequence optimization tasks.

Pre-trained protein language models have demonstrated significant applicability in different protein engineering task. A general usage of these pre-trained transformer models latent representation is to use a mean pool across residue positions to reduce the feature dimensions to further downstream tasks such as predicting bio-physics properties or other functional behaviours. In this paper we provide a two-fold contribution to machine learning (ML) driven drug design. Firstly, we demonstrate the power of sparsity by promoting penalization of pre-trained transformer models to secure more robust and accurate melting temperature (Tm) prediction of single-chain variable fragments with a mean absolute error of 0.23C. Secondly, we demonstrate the power of framing our prediction problem in a probabilistic framework. Specifically, we advocate for the need of adopting probabilistic frameworks especially in the context of ML driven drug design.

Probabilistic models often use neural networks to control their predictive uncertainty. However, when making out-of-distribution (OOD)} predictions, the often-uncontrollable extrapolation properties of neural networks yield poor uncertainty predictions. Such models then don't know what they don't know, which directly limits their robustness w.r.t unexpected inputs. To counter this, we propose to explicitly train the uncertainty predictor where we are not given data to make it reliable. As one cannot train without data, we provide mechanisms for generating pseudo-inputs in informative low-density regions of the input space, and show how to leverage these in a practical Bayesian framework that casts a prior distribution over the model uncertainty. With a holistic evaluation, we demonstrate that this yields robust and interpretable predictions of uncertainty while retaining state-of-the-art performance on diverse tasks such as regression and generative modelling

Standard laser based fire detection systems are often based on measuring variation of optical signal amplitude. However, mechanical noise interference and loss from dust and steam can obscure the detection signal, resulting in faulty results or inability to detect a potential fire. The presented fire detection technology will allow the detection of fire in harsh and dusty areas, which are prone to fires, where current systems show limited performance or are unable to operate. It is not the amount of light nor its wavelength that is used for detecting fire, but how the refractive index randomly fluctuates due to the heat convection from the fire. In practical terms this means that light obstruction from ambient dust particles will not be a problem as long as a small fraction of the light is detected and that fires without visible flames can still be detected. The standalone laser system consists of a Linux-based Red Pitaya system, a cheap 650 nm laser diode, and a PIN photo-detector. Laser light propagates through the monitored area and reflects off a retroreflector generating a speckle pattern. Every 3 seconds time traces and frequency noise spectra are measured and 8 descriptors are deduced to identify a potential fire. Both laboratory and factory acceptance tests have been performed with success., Comment: 6 pages, 5 figures