arXiv:2606. 30170v1 Announce Type: cross Abstract: Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets.
Exploring the chemical space of flexible molecules remains challenging because the vast number of possible compounds and conformations, together with the increasing cost and limited generalization of...
arXiv:2609.16527v1 Announce Type: cross Abstract: Exploring the chemical space of flexible molecules remains challenging because the vast number of possible compounds and conformations, together with...
BOOM is a new benchmark for evaluating out‑of‑distribution (OOD) molecular property predictions in machine learning. It provides chemically‑informed tests across common property prediction tasks and assesses over 150 model‑task combinations. The study shows that current models, including chemical foundation models, struggle to generalize OOD, with the best model still exhibiting three times higher error than in‑distribution predictions.
arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.
The paper introduces NSA-Bench, a public benchmark for predicting nano self‑assembly (NSA) between molecular pairs, framing it as a binary classification problem. It presents NSA‑Net, a multimodal learning framework that fuses graph topology, sequence semantics, and physicochemical descriptors to predict self‑assembly, achieving high ROC‑AUC scores and outperforming existing baselines. The study also demonstrates how NSA‑Net’s predictions can guide experimental formulation refinement through an NSA‑Agent case study.
arXiv:2607. 03787v1 Announce Type: new Abstract: Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery.
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:2606. 02662v1 Announce Type: cross Abstract: Machine learning has accelerated quantum chemistry but is hindered by the prohibitive cost of generating high fidelity training data.
The paper presents a closed‑loop molecule generation pipeline that iteratively retrains on new quantum‑chemical simulation data, overcoming limitations of static generative models. This approach produces molecules whose properties extend up to 0.44 standard deviations beyond the training set and improves out‑of‑distribution classification accuracy by 79%. By conditioning on thermodynamic stability during the loop, the method yields a 3.5‑fold increase in the proportion of stable, potentially synthesizable molecules.
arXiv:2607. 11701v1 Announce Type: cross Abstract: Quantitative Structure-Activity Relationship ($\mathtt{QSAR}$) modeling is a foundational computational methodology in early-stage drug discovery, heavily relied upon for predicting compound toxicity, bioavailability, and therapeutic potential.
arXiv:2606. 17077v1 Announce Type: cross Abstract: Proton dissociation constants (pKa) are critical for functional molecule discovery and molecular modeling.
arXiv:2607. 28553v1 Announce Type: new Abstract: Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery.