arXiv:2608. 13800v1 Announce Type: new Abstract: Transition path sampling (TPS) aims to efficiently generate rare molecular transition trajectories between metastable states and is essential for understanding biomolecular mechanisms.
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).
The paper introduces MCTH (Monte Carlo Tree Hallucination), an inference-only framework that performs all‑atom biomolecular sequence‑structure co‑design by treating pretrained folding and inverse‑folding models as black‑box operators. MCTH uses Monte Carlo Tree Search to allocate a fixed inference budget across competing design trajectories, incorporating model confidence, uncertainty, and cross‑expert consensus. Experiments across protein‑RNA, protein‑DNA, protein‑protein, and protein‑ligand design show that adaptive search outperforms simpler sampling strategies, and evaluations with AlphaFold3 and Chai‑1 demonstrate transferability beyond the search‑time oracle.
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.
arXiv:2510. 08906v2 Announce Type: replace-cross Abstract: Training set sampling methods are used to improve model performance and lower data costs in machine learning problems relevant to chemistry.
arXiv:2604. 13213v2 Announce Type: replace-cross Abstract: Rare events such as conformational changes in biomolecules, phase transitions, and chemical reactions are central to the behavior of many physical systems, yet they are extremely difficult to study computationally because unbiased simulations seldom produce them.
Studying the dynamical behavior of a system often depends on characterizing how it transitions between long-lived states. Because such transitions are rare, observing them usually requires specialized...
The paper introduces GenAIMMD, an iterative algorithm that learns the committor function and trains a conditioned Boltzmann Generator to generate uncorrelated transition paths without prior knowledge of the reaction coordinate. This method combines transition path sampling with committor learning, enabling fully parallelizable sampling. Benchmarks on a toy model and a polymer system show a substantial performance improvement over standard TPS.
arXiv:2607. 19044v1 Announce Type: new Abstract: Leveraging large language models (LLMs) for molecular generation has shown remarkable potential in chemical and drug design.
arXiv:2609.36683v1 Announce Type: new Abstract: Molecular optimization is inherently iterative: a candidate is proposed, evaluated against several objectives, and revised while preserving a relations...
Budgeted Quotient-Residual Guidance (QRG) is an inference-time correction that enables quotient-based lead‑optimization objectives—such as distances, contacts, and anchored substructures—to be actively used with frozen pocket‑conditioned molecular diffusion models without retraining. QRG lifts quotient covectors to metric‑horizontal ambient directions and delivers them through a trust budget set by the sampler’s step norm, providing a closed‑form sampler‑budget update and a product‑budget split for section and residual controls. Experiments on frozen TargetDiff backbones show that QRG improves ligand‑generation quality on fragment growing, scaffold hopping, and linker design while preserving novelty and diversity.
arXiv:2609.00189v1 Announce Type: new Abstract: Goal-directed optimization is essential for steering molecular generators to propose candidates with desired properties. However, it is often implement...
arXiv:2606. 04100v1 Announce Type: new Abstract: Machine learning interatomic potentials (MLIPs) enable efficient and accurate atomistic simulations but depend critically on the quality and diversity of the training data.