Designing protein sequences of both high fitness and novelty is a challenging task in data-efficient protein engineering. Exploration beyond wild-type neighborhoods often leads to biologically implausible sequences or relies on surrogate models that lose fidelity in novel regions. Here, we propose PROSPERO, an active learning framework in which a frozen pre-trained generative model is guided by a surrogate updated from oracle feedback. By integrating fitness-relevant residue selection with biologically-constrained Sequential Monte Carlo sampling, our approach enables exploration beyond wild-type neighborhoods while preserving biological plausibility. We show that our framework remains effective even when the surrogate is misspecified. PROSPERO consistently outperforms or matches existing methods across diverse protein engineering tasks, retrieving sequences of both high fitness and novelty.

Designing de novo 3D molecules with desirable properties remains a fundamental challenge in drug discovery and molecular engineering. While diffusion models have demonstrated remarkable capabilities in generating high-quality 3D molecular structures, they often struggle to effectively control complex multi-objective constraints critical for real-world applications. In this study, we propose an uncertaintyaware Reinforcement Learning (RL) framework to guide the optimization of 3D molecular diffusion models toward multiple property objectives while enhancing the overall quality of the generated molecules. Our method leverages surrogate models with predictive uncertainty estimation to dynamically shape reward functions, facilitating balance across multiple optimization objectives. We comprehensively evaluate our framework across three benchmark datasets and multiple diffusion model architectures, consistently outperforming baselines for molecular quality and property optimization. Additionally, Molecular Dynamics (MD) simulations and ADMET profiling of top generated candidates indicate promising drug-like behavior and binding stability, comparable to known Epidermal Growth Factor Receptor (EGFR) inhibitors. Our results demonstrate the strong potential of RL-guided generative diffusion models for advancing automated molecular design.

Many real-world black-box optimization problems have multiple conflicting objectives. Rather than attempting to approximate the entire set of Pareto-optimal solutions, interactive preference learning, i.e., optimization with a decision maker in the loop, allows us to focus the search on the most relevant subset. However, few previous studies have exploited the fact that utility functions are typically monotonic. In this paper, we address the Bayesian Optimization with Preference Exploration (BOPE) problem and propose using a neural network ensemble as a utility surrogate model. This approach naturally integrates monotonicity and allows learning the decision maker's preferences from pairwise comparisons. Our experiments demonstrate that the proposed method outperforms state-of-the-art approaches and is robust to noise in utility evaluations. An ablation study highlights the critical role of monotonicity in enhancing performance.

Neural Architecture Search (NAS) aims to identify high-performance networks within a defined search space. Training-free metrics have been proposed to estimate network performance without actual training, reducing NAS deployment costs. However, individual training-free metrics often capture only partial architectural features, and their estimation capabilities are different in various tasks. Combining multiple training-free metrics has been explored to enhance scalability across tasks. Yet, these methods typically optimize global metric combinations over the entire search space, overlooking the varying sensitivities of different architectures to specific metrics, which may limit the final architectures' performance. To address these challenges, we propose the Per-Architecture Training-Free Metric Optimization NAS (PO-NAS) algorithm.

Algorithm configuration, which involves selecting algorithm parameters based on sampled problem instances, is a crucial step in applying modern algorithms such as SAT solvers. Although prior work has attempted to understand the theoretical foundations of algorithm configuration, we still lack a comprehensive understanding of why practical algorithm configurators exhibit strong generalization performances in real-world scenarios. In this paper, through the lens of machine learning theory, we provide an algorithm-dependent generalization bound for the widely used model-based algorithm configurators under mild assumptions. Our approach is based on the algorithmic stability framework for generalization bounds. To the best of our knowledge, this is the first generalization bound that applies to a model closely approximating practical model-based algorithm configurators.

Adversarial examples crafted on one model often exhibit poor transferability to others, hindering their effectiveness in black-box settings. This limitation arises from two key factors: (i) decision-boundary variation across models and (ii) representation drift in feature space. We address these challenges through a new perspective that frames transferability for untargeted attacks as a consensus-robust optimization problem: adversarial perturbations should remain effective across a neighborhood of plausible target models. To model this uncertainty, we introduce two complementary perturbation channels: a parameter channel, capturing boundary shifts via weight perturbations, and a representation channel, addressing feature drift via stochastic blending of clean and adversarial activations. We then propose CORTA (COnsensus-Robust Transfer Attack), a lightweight attack instantiated from this robust formulation using two first-order strategies: (i) sensitivity regularization based on the squared Frobenius norm of logits' Jacobian with respect to weights, and (ii) Monte Carlo sampling for blended feature representations. Our theoretical analysis provides a certified lower bound linking these approximations to the robust objective. Extensive experiments on CIFAR-100 and ImageNet show that CORTA significantly outperforms state-of-the-art transfer-based methods-- including ensemble approaches--across CNN and Vision Transformer targets. Notably, CORTA achieves a 19.1 percentage-point gain in transfer success rate over the best prior method while using only a single surrogate model.

Deep neural networks are vulnerable to adversarial examples that exhibit transferability across various models. Numerous approaches are proposed to enhance the transferability of adversarial examples, including advanced optimization, data augmentation, and model modifications. However, these methods still show limited transferability, particularly in cross-architecture scenarios, such as from CNN to ViT. To achieve high transferability, we propose a technique termed Spatial Adversarial Alignment (SAA), which employs an alignment loss and leverages a witness model to fine-tune the surrogate model. Specifically, SAA consists of two key parts: spatial-aware alignment and adversarial-aware alignment.

Offline multi-objective optimization aims to identify Pareto-optimal solutions given a dataset of designs and their objective values. In this work, we propose a preference-guided diffusion model that generates Pareto-optimal designs by leveraging a classifier-based guidance mechanism. Our guidance classifier is a preference model trained to predict the probability that one design dominates another, directing the diffusion model toward optimal regions of the design space. Crucially, this preference model generalizes beyond the training distribution, enabling the discovery of Pareto-optimal solutions outside the observed dataset. We introduce a novel diversity-aware preference guidance, augmenting Pareto dominance preference with diversity criteria. This ensures that generated solutions are optimal and well-distributed across the objective space, a capability absent in prior generative methods for offline multi-objective optimization. We evaluate our approach on various continuous offline multi-objective optimization tasks and find that it consistently outperforms other inverse/generative approaches while remaining competitive with forward/ surrogate-based optimization methods. Our results highlight the effectiveness of classifier-guided diffusion models in generating diverse and high-quality solutions that approximate the Pareto front well.

Surrogate models are widely used to approximate complex systems across science and engineering to reduce computational costs. Despite their widespread adoption, the field lacks standardisation across key stages of the modelling pipeline, including data sampling, model selection, evaluation, and downstream analysis. This fragmentation limits reproducibility and cross-domain utility - a challengefurther exacerbated by the rapid proliferation of AI-driven surrogate models. We argue for the urgent need to establish a structured reporting standard, the Surrogate Model Reporting Standard (SMRS), that systematically captures essential design and evaluation choices while remaining agnostic to implementation specifics. By promoting a standardised yet flexible framework, we aim to improve the reliabilityof surrogate modelling, foster interdisciplinary knowledge transfer, and, as a result, accelerate scientific progress in the AI era.

Deep neural networks are vulnerable to adversarial examples that exhibit transferability across various models. Numerous approaches are proposed to enhance the transferability of adversarial examples, including advanced optimization, data augmentation, and model modifications. However, these methods still show limited transferability, partiovovocularly in cross-architecture scenarios, such as from CNN to ViT. To achieve high transferability, we propose a technique termed Spatial Adversarial Alignment (SAA), which employs an alignment loss and leverages a witness model to fine-tune the surrogate model. Specifically, SAA consists of two key parts: spatial-aware alignment and adversarial-aware alignment.