arXiv subjects

Aleksandra Kalisz

Publications and source records attributed to Aleksandra Kalisz.

6 recordsLinked to original sources

arXiv2026

Search at the Cost of Sampling: Nearly-Instant Latent Space Bayesian Optimization

Generative models are increasingly central to many de novo discovery pipelines, in which designs are generated at scale and filtered through virtual screens to determine a set of candidates to experimentally validate. While Bayesian optimization (BO) is a natural fit for this setting, as it uses past evaluations to guide future proposals, the computational overhead required for its sequential decision-making becomes a bottleneck when virtual screens are relatively cheap. We make BO practical in this regime by exploiting the unique combination of a linear model constrained to a spherical domain where high-dimensional latents concentrate. We build off recent work justifying the use of linear surrogates, while deriving nearly closed-form solutions to the surrogate modelling and acquisition problems that exploit spherical symmetry. The result is at least a 100x speedup over state-of-the art baselines, with matching or improved performance across molecular and image generation benchmarks. Altogether, our method makes BO a practical drop-in for de novo pipelines where it was previously too slow to consider.

cs.LG↗

arXiv2026

How to Spend Your Oracle Budget: Practical Guidance for Protein Structure Prediction Models

Foundation models for protein structure prediction remain unreliable on certain targets. External oracles can flag and correct these failures, but biological oracles are expensive, making oracle budget a critical constraint. Existing guidance methods, such as FK-steering, DPO, and Best K-of-N sampling, differ in how they spend this budget, yet no systematic comparison exists to guide method selection. To bridge this gap, we benchmark these methods alongside the recently proposed Optimisation Over Outputs (O3), which applies off-the-shelf optimisers within a generative model's latent subspace. We extend the usage of O3 to protein structure prediction models. Overall, our work provides the first practical reference for oracle budget-aware guidance. Our evaluation on two protein targets, calmodulin (1CLL) and E. coli aspartate transcarbamoylase (9EEH), reveals that no single method consistently dominates across all budgets and oracles. Specifically, O3 proves most effective at low oracle budgets, while FK-steering and DPO demonstrate improved performance as the budget increases. We distil these findings into actionable recommendations for practitioners operating under real-world oracle-budget constraints.

cs.AI↗

arXiv2026

DiscoGen: Procedural Generation of Algorithm Discovery Tasks in Machine Learning

Automating the development of machine learning algorithms has the potential to unlock new breakthroughs. However, our ability to improve and evaluate algorithm discovery systems has thus far been limited by existing task suites. They suffer from many issues, such as: poor evaluation methodologies; data contamination; and containing saturated or very similar problems. Here, we introduce DiscoGen, a procedural generator of algorithm discovery tasks for machine learning, such as developing optimisers for reinforcement learning or loss functions for image classification. Motivated by the success of procedural generation in reinforcement learning, DiscoGen spans billions of tasks of varying difficulty and complexity from a range of machine learning fields. These tasks are specified by a small number of configuration parameters and can be used to optimise algorithm discovery agents (ADAs). We present DiscoBench, a fixed, small subset of DiscoGen tasks for principled evaluation of ADAs. Finally, we propose a number of ambitious, impactful research directions enabled by DiscoGen, and demonstrate its use for ADA optimisation through scaling experiments for automated prompt tuning. DiscoGen is released open-source at https://github.com/AlexGoldie/discogen.

cs.LG↗

arXiv2026

Sample-Efficient Optimisation over the Outputs of Generative Models

Modern generative AI models, such as diffusion and flow matching models, can sample from rich data distributions. However, many applications, especially in science and engineering, require more than drawing samples from the model distribution: they require searching within this distribution for samples that optimise task-specific criteria. In this work, we propose O3 (Optimisation Over the Outputs of Generative Models), a method for sample-efficient black-box optimisation over continuous-variable diffusion and flow-matching models. O3 is built around surrogate latent spaces: low-dimensional Euclidean embeddings that can be extracted from a generative model without additional training. The resulting representations have controllable dimensionality and support the direct application of standard optimisation algorithms. We show, on image and protein design tasks, that surrogate-space optimisation finds substantially higher-scoring samples than standard sampling or optimisation in the original latent space. Our method is model- and optimiser-agnostic, incurs negligible additional cost over standard generation, and requires no retraining or fine-tuning of the generative model.

stat.ML↗

arXiv2025

ADIOS: Antibody Development via Opponent Shaping

Anti-viral therapies are typically designed to target only the current strains of a virus, a myopic response. However, therapy-induced selective pressures drive the emergence of new viral strains, against which the original myopic therapies are no longer effective. This evolutionary response presents an opportunity: our therapies could both defend against and actively influence viral evolution. This motivates our method ADIOS: Antibody Development vIa Opponent Shaping. ADIOS is a meta-learning framework where the process of antibody therapy design, the outer loop, accounts for the virus's adaptive response, the inner loop. With ADIOS, antibodies are not only robust against potential future variants, they also influence, i.e., shape, which future variants emerge. In line with the opponent shaping literature, we refer to our optimised antibodies as shapers. To demonstrate the value of ADIOS, we build a viral evolution simulator using the Absolut! framework, in which shapers successfully target both current and future viral variants, outperforming myopic antibodies. Furthermore, we show that shapers modify the distribution over viral evolutionary trajectories to result in weaker variants. We believe that our ADIOS paradigm will facilitate the discovery of long-lived vaccines and antibody therapies while also generalising to other domains. Specifically, domains such as antimicrobial resistance, cancer treatment, and others with evolutionarily adaptive opponents. Our code is available at https://github.com/olakalisz/adios.

q-bio.PE↗

arXiv2020

Learning to Prune Deep Neural Networks via Reinforcement Learning

This paper proposes PuRL - a deep reinforcement learning (RL) based algorithm for pruning neural networks. Unlike current RL based model compression approaches where feedback is given only at the end of each episode to the agent, PuRL provides rewards at every pruning step. This enables PuRL to achieve sparsity and accuracy comparable to current state-of-the-art methods, while having a much shorter training cycle. PuRL achieves more than 80% sparsity on the ResNet-50 model while retaining a Top-1 accuracy of 75.37% on the ImageNet dataset. Through our experiments we show that PuRL is also able to sparsify already efficient architectures like MobileNet-V2. In addition to performance characterisation experiments, we also provide a discussion and analysis of the various RL design choices that went into the tuning of the Markov Decision Process underlying PuRL. Lastly, we point out that PuRL is simple to use and can be easily adapted for various architectures.

cs.AI↗