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.
By Xujun Che, Xiuxia Du, Depeng Xu
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.
By Yunhua Zhong, Yixuan Tang, Yifan Li, Pan Liu, Zhiwen Yang, Jie Yang, Jun Xia
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.
By Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar, Magdalena Lederbauer, Shuiwang Ji, Runzhong Wang, Connor W. Coley
arXiv:2607. 19816v1 Announce Type: cross Abstract: Determining molecular structures from spectroscopic data remains fundamentally challenging because the inverse problem is intrinsically underdetermined: individual spectra are sparse, low-dimensional, and encode only partial structural evidence relative to the vast space of possible molecules.
By Chengchun Liu, Zhiyuan Yan, Li Yuan, Hao Li, Boxuan Zhao, Yonghong Tian, Bartosz A. Grzybowski, Fanyang Mo
arXiv:2603. 10950v2 Announce Type: replace Abstract: Machine learning methods for identifying molecular structures from tandem mass spectra (MS/MS) have advanced rapidly, yet current approaches still exhibit significant error rates.
By Mira J\"urgens, Gaetan De Waele, Morteza Rakhshaninejad, Willem Waegeman
arXiv:2603. 25062v2 Announce Type: replace Abstract: Autoregressive molecular models assign probability to molecular serializations even though chemical identity is invariant to serialization.
By Xinyu Wang, Fei Dou, Jinbo Bi, Minghu Song