arXiv AI

FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction

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 Machine Learning

Jun 19

MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule 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.

By Hongxuan Liu, Roman Bushuiev, Ivy Lightheart, Mrunali Manjrekar, Anton Bushuiev, Magdalena Lederbauer, Filip Jozefov, Yinkai Wang, Soha Hassoun, Josef Sivic, James Taylor, Runzhong Wang, David Healey, Tom\'a\v{s} Pluskal, Connor W. Coley

benchmarks

arXiv Machine Learning

Jul 1

ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table

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.

By Jacob W. Toney, Samir Darouich, Yiran Wang, Aaron G. Garrison, Johannes K\"astner, Heather J. Kulik

llms benchmarks

arXiv Machine Learning

Jul 28

MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model

arXiv:2607. 23607v1 Announce Type: new Abstract: Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry.

By Xin Zhao, Yumin Liu, Zhuo Li, Weichu Zheng, Feng Zhu, Xiaokang Yang, Yaohui Jin, Yanyan Xu

llms fine-tuning safety

arXiv Machine Learning

Jul 7

MARLIN: De Novo Molecular Structure Elucidation from Tandem Mass Spectra without a Ground-Truth Formula

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

llms diffusion benchmarks

arXiv Machine Learning

Jun 9

Automating the Expert Eye: A System-Agnostic Deep Learning Framework for Rare Event Discovery in Imbalanced Force Spectroscopy

arXiv:2606. 09541v1 Announce Type: cross Abstract: Single-Molecule Force Spectroscopy (SMFS) provides unprecedented insights into biomolecular mechanics, yet the high-throughput generation of force-extension trajectories creates a severe data curation bottleneck.

By Jorge Rodriguez-Ramos

efficiency

arXiv Machine Learning

Aug 11

When should we trust the annotation? Selective prediction for molecular structure retrieval from mass spectra

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

diffusion benchmarks

arXiv Machine Learning

Jun 30

GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem

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.

By Rui-Xi Wang, Runzhong Wang, Connor W. Coley

llms computer-vision fine-tuning benchmarks

arXiv Machine Learning

6d ago

Large-scale AI-Ready Data for Anti-Cancer Drug Response Modeling

arXiv:2608. 11444v1 Announce Type: cross Abstract: Drug response prediction (DRP) models are an active area of research in pharmacogenomics, with growing potential to accelerate the identification of effective anticancer drugs.

By Vincent Lavelle, Yitan Zhu, Kaitlyn Marlor, Thomas Brettin, Rick Stevens

benchmarks

arXiv Machine Learning

Jul 23

Hypothesis-and-Refinement Learning of Organic Structures from Multimodal Spectroscopic Data

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

fine-tuning multimodal benchmarks

arXiv AI

5d ago

Simulation-to-real transfer learning for infrared spectroscopic chemical sensing and analysis from molecules to complex samples

arXiv:2608. 13341v1 Announce Type: cross Abstract: Infrared (IR) spectroscopy is widely used for chemical sensing, but extracting reliable chemical information from spectra remains challenging.

By Yusen Tan, Yixuan Chen, Zheng Fang, Pan Liu, Yifan Li, Qinyu Guo, Zhedong Lin, Yuqiang Li, Xiangxiang Zeng, Tong Wang, Jun Xia

fine-tuning safety

arXiv Machine Learning

2d ago

Recent Advances in Deep Learning-Based Drug-Target Binding Affinity Prediction

arXiv:2608. 13797v1 Announce Type: new Abstract: Computational approaches to drug discovery involve multiple sub-problems, and among them, drug-target binding affinity prediction plays an important role.

By Jafin Khan, Md Hossain Shuvo

multimodal benchmarks safety

arXiv Machine Learning

Jun 18

KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Prediction

arXiv:2506. 13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery.

By Han Liu, Keyan Ding, Peilin Chen, Yinwei Wei, Liqiang Nie, Dapeng Wu, Shiqi Wang

rag benchmarks safety

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