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:2606. 18961v1 Announce Type: new Abstract: Protein language models (PLMs) have emerged as powerful tools for controllable biomolecular design, yet their post-training adaptation typically relies on costly wet-lab validation or curated preference datasets.
By Lanqing Li, Shentong Mo, Yang Yu, Pheng-Ann Heng
Protein language models (PLMs) have emerged as powerful tools for controllable biomolecular design, yet their post-training adaptation typically relies on costly wet-lab validation or curated preference datasets. To overcome this supervision bottleneck, we introduce unsupervised reward optimization of PLMs, a comprehensive framework for steerable protein generation without ground-truth labels.
arXiv:2606. 24990v1 Announce Type: new Abstract: Reinforcement Learning (RL) has become a powerful paradigm for de novo molecular design, enabling Chemical Language Models (CLMs) to navigate and explore the chemical space while optimizing specific desired properties.
By Borja Medina, Jon Paul Janet
arXiv:2607. 19044v1 Announce Type: new Abstract: Leveraging large language models (LLMs) for molecular generation has shown remarkable potential in chemical and drug design.
By Mingxuan Ouyang, Hao Lan, Wanyu Lin
arXiv:2607. 02834v1 Announce Type: new Abstract: Molecular optimization often starts from a pretrained generative model that captures a broad prior over valid molecular structures.
By Trevor Chen, Ariel Dai, Jason Yang, Riccardo De Santi, Daniel Khalil, Wenda Chu, Nate Gruver, Pranav Murugan, Alexander F. G. Goldberg, Maruan Al-Shedivat, Yisong Yue
arXiv:2606. 30335v1 Announce Type: new Abstract: Autonomous scientific discovery systems increasingly use large language models (LLMs) to propose new hypotheses, but many such systems condition primarily on experimental memory: archives of high-scoring candidates or heuristic summaries of recent trials.
By Xuening Wu, Shan Yu, Qianya Xu, Shenqin Yin
arXiv:2606. 29182v1 Announce Type: new Abstract: Open-ended scientific discovery with large language models (LLMs) increasingly operates as a long-horizon loop of hypothesis search and verification, where a reward signal guides which hypotheses to test next.
By Dhruv Agarwal, Reece Adamson, Andrew McCallum, Peter Clark, Ashish Sabharwal, Bodhisattwa Prasad Majumder
arXiv:2602. 06448v2 Announce Type: replace-cross Abstract: Large Language Model (LLM)-based scientific agents have accelerated scientific discovery, yet they often suffer from significant inefficiencies due to adherence to fixed initial priors.
By Yingming Pu, Tao Lin, Hongyu Chen
arXiv:2608. 09696v1 Announce Type: new Abstract: Predicting the answer to interventional ``what if'' questions --- the outcome of an action never taken --- requires a \emph{mechanistic}, causal model, not a curve fit; and learning such a model requires \emph{experiments}, because passive data leaves its mechanisms unidentified.
By Kevin Murphy
arXiv:2606. 11256v1 Announce Type: cross Abstract: Designing molecules with target properties is most useful when candidate structures are accompanied by feasible synthetic routes.
By C\'esar Ojeda, Darius A. Faroughy, Maryam Karimi, Payam Zarrintaj, Mir Mehdi Seyedebrahimi, Mart\'in Carballo-Pacheco