The paper introduces a new Bayesian optimization approach tailored for generative models used in de novo discovery pipelines. By employing a linear surrogate model constrained to a spherical domain—where high‑dimensional latent vectors naturally concentrate—the authors derive nearly closed‑form solutions for both surrogate modeling and acquisition, achieving at least a 100‑fold speedup over existing methods. This acceleration enables Bayesian optimization to be used as a practical drop‑in component in pipelines that previously found it too slow to consider.
arXiv:2606. 09664v1 Announce Type: new Abstract: Bayesian optimization (BO) is a central tool for sample-efficient design, and latent-space Bayesian optimization (LSBO) extends it to structured objects such as molecules and proteins.
arXiv:2607. 12488v1 Announce Type: new Abstract: Molecular optimization in drug discovery, materials design, and catalysis requires searching vast chemical spaces under tight evaluation budgets, since high-fidelity oracles and experimental measurements are costly.
The paper introduces Gradient-based Sample Selection Bayesian Optimization (GSSBO), a method that builds the Gaussian process surrogate on a strategically chosen subset of samples rather than the full dataset. By using gradient information to eliminate redundant points while keeping diversity and representativeness, GSSBO achieves sublinear regret bounds and reduces the cubic computational cost of standard BO. Experiments on synthetic and real-world tasks show that this approach maintains comparable optimization performance while significantly cutting GP fitting time and resource usage.
arXiv:2607. 29225v1 Announce Type: new Abstract: Bayesian Optimization (BO) is widely adopted for data-efficient optimization in scientific and engineering applications, yet its computational cost is rarely evaluated alongside optimization performance.
arXiv:2606. 26657v1 Announce Type: new Abstract: Identifying high-utility candidates from massive discrete spaces under expensive evaluations is a recurring challenge across the sciences, with structure-based drug discovery as a prominent example.
arXiv:2406. 03616v5 Announce Type: replace-cross Abstract: Novelty search (NS) aims to uncover diverse system behaviors through simulation or experiment without requiring a pre-specified scalar objective.
The paper investigates nonlinear dimensionality reduction for Bayesian optimisation (BO) by transforming high‑dimensional black‑box optimisation problems into a sequence of low‑dimensional latent‑space BO (LSBO) tasks. It extends earlier linear embedding approaches by using variational autoencoders (VAEs), deep metric loss, and adaptive retraining to better capture nonlinear structure, and couples LSBO with sequential domain reduction (SDR‑LSBO) to progressively narrow search domains. Experiments on GPU‑accelerated BoTorch with Matérn‑5/2 Gaussian‑process surrogates show that VAE‑based LSBO outperforms adaptive linear embeddings, and the authors provide a theoretical analysis of latent‑space error versus representation gap under PAC‑Bayes conditions.
arXiv:2608. 04113v1 Announce Type: cross Abstract: Black-box optimization is a ubiquitous problem in science and engineering, often dealing with expensive objective functions with cheaper lower-fidelity proxies available.
arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.
arXiv:2607. 23404v1 Announce Type: new Abstract: Self-driving laboratories increasingly rely on multi-fidelity Bayesian optimization (MFBO) to balance cheap, approximate evaluations against scarce, expensive ones, with a predictive surrogate at its core.
arXiv:2609.37381v1 Announce Type: new Abstract: Neural simulation-based inference (SBI) has been widely successful in inferring a relatively small number of interpretable parameters from potentially...
arXiv:2608.22967v1 Announce Type: new Abstract: Practical molecular inverse design is rarely a one-shot generation problem; it often takes the form of closed-loop candidate-pool enrichment, where und...