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.
By Mohammad Haddadnia, Yuvan Chali, Abhilash Jayaraj, Constance Kraay, Joana Reis, Felix Strieth-Kalthoff, Haribabu Arthanari
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.
By Sarina Kopf, Cristina Nevado, Philippe Schwaller
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.
By Jaewook Lee, Ethan Errington, Christian D. Lorenz, Miao Guo
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.
By Gustavo Sutter, Hao Wang, Luis Ricardez-Sandoval, Pascal Poupart, Agustinus Kristiadi
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.
By Wei-Ting Tang, Ankush Chakrabarty, Joel A. Paulson
arXiv:2607. 10669v1 Announce Type: new Abstract: Bayesian optimization is increasingly used to guide data-efficient experimentation in chemistry, materials science, and related laboratory settings, but its practical performance depends strongly on how well surrogate-model assumptions match the geometry and noise structure of the underlying objective.
By L. A. Zhukov, E. V. Shaburova, D. V. Antonets
arXiv:2608. 04333v1 Announce Type: new Abstract: Large language model (LLM) configuration evaluation is challenging due to limited evaluation budgets, varying costs, and multiple competing objectives.
By Bo Xue, Zhi Hong, Jiayi Li, Yuanyu Wan, Ji Cheng, Shuang Qiu
Accurate protein-ligand binding affinity prediction is central to computational drug discovery, yet modern docking engines frequently disagree without indicating which prediction to trust. Consensus scoring and ensemble methods improve mean accuracy but treat all predictions identically without interpretable confidence measures or uncertainty decomposition, ignoring the chemical context of each protein-ligand pair.
arXiv:2608. 15669v1 Announce Type: new Abstract: Scientific discovery often involves optimising expensive-to-evaluate objectives over vast, structured, and open-ended hypothesis spaces, such as molecules, protein sequences, and computer programs.
By Zhongwei Yu, Yan Song, Xue Yan, Anjie Liu, Xingyu Lu, Yihang Chen, Huichi Zhou, Siyuan Guo, Luoyang Sun, Sihan Chen, Xiangning Yu, Jun Wang
arXiv:2606. 01220v1 Announce Type: cross Abstract: Generating molecules that simultaneously satisfy drug-like properties and conform to the 3D structure of a target protein is a core challenge in structure-based drug design (SBDD).
By Guang Lin, Shikui Tu, Lei Xu
arXiv:2607. 17601v1 Announce Type: cross Abstract: Accurate protein-ligand binding affinity prediction is central to computational drug discovery, yet modern docking engines frequently disagree without indicating which prediction to trust.
By Yongchan Hong, Defu Cao, Wenjin Liu, Thomas Ku, Jordy Homing Lam, Emily Nguyen, Willie Neiswanger, Vsevolod Katritch, Yan Liu
arXiv:2606. 06984v1 Announce Type: new Abstract: This paper presents a general acceleration mechanism for multi-objective Bayesian optimisation (MOBO) that leverages Gaussian process predictive gradients as auxiliary signals.
By Alma Rahat, Tinkle Chugh, Jonathan Fieldsend, Richard Allmendinger