arXiv:2604. 16648v2 Announce Type: replace Abstract: Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging.
arXiv:2607. 04774v1 Announce Type: new Abstract: Untargeted tandem mass spectrometry (MS/MS) detects thousands of small molecules per biological sample, yet most go unidentified because they are absent from spectral libraries.
arXiv:2607. 23607v1 Announce Type: new Abstract: Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry.
The paper introduces MSAlign, a lightweight model that aligns frozen foundation models for mass spectra (DreaMS) and molecules (MolDeBERTa) to improve metabolite identification from MS/MS spectra. It presents a unified framework for representation alignment and contrastive learning, demonstrates that a score fusion strategy further boosts performance at minimal cost, and addresses evaluation challenges by quantifying distribution shift in data splitting strategies. All resources, including datasets, splits, and code, are publicly released to promote reproducible research.
arXiv:2606. 29161v1 Announce Type: new Abstract: Predicting tandem mass spectra (MS/MS) from molecular structures represents a central task in analytical chemistry with direct relevance to clinical metabolomics, systems biology, and adjacent disciplines.
arXiv:2602. 22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice.
arXiv:2606. 00401v1 Announce Type: cross Abstract: Simulating large molecular systems comprising thousands of atoms requires highly scalable methodologies.
arXiv:2510.03095v4 Announce Type: replace Abstract: Diffusion- and flow-based generative models have recently demonstrated strong performance in protein backbone generation tasks, offering unpreceden...
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:2603. 23398v3 Announce Type: replace-cross Abstract: Generative modeling of discrete data, such as graphs, underpins many scientific and industrial applications, including molecular discovery and materials design.
arXiv:2607. 03787v1 Announce Type: new Abstract: Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery.
arXiv:2606. 19624v1 Announce Type: new Abstract: Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery.
Transport-Coupled Bayesian Flows for Molecular Graph Generation (TopBF) addresses a key mismatch in existing diffusion models for molecular graph generation by eliminating the need for hard discretization during sampling. The framework generates graphs directly in continuous parameter distributions, learns graph topology via a Quasi-Wasserstein optimal‑transport coupling with geodesic costs, and enables property‑conditioned generation without retraining. Experiments on QM9 and ZINC250k show that TopBF achieves higher structural fidelity and more efficient generation compared to prior methods.