GEMS (Guided Editing of Molecular Structures) is a new method for refining candidate small‑molecule structures from molecular formulas and tandem mass spectra. It uses learned 2‑switch bond edits that preserve the formula and valence, guided by a neural policy trained on shortest edit paths and fingerprint predictions from the MIST model. In benchmark tests, GEMS outperforms existing baselines, achieving higher Hit@1/Hit@10 rates and dramatically faster identification times compared to prior approaches.
arXiv:2607. 23607v1 Announce Type: new Abstract: Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry.
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:2604. 27810v2 Announce Type: replace Abstract: Computational molecular representations underpin virtual screening, property prediction, and materials discovery.
arXiv:2610.19123v1 Announce Type: new Abstract: Generating novel molecules with desired properties is a central challenge in drug discovery. Although foundational work focused on de novo generation,...
The paper introduces MolPAIR, a framework that enhances tabular foundation models (TFMs) for predicting molecular properties under structural shifts by incorporating molecule-level and molecular-pair contexts without task‑specific parameter updates. MolPAIR refines initial predictions from a global TFM by using a second frozen TFM to predict differences in prediction errors between a query molecule and labeled reference molecules. Experiments on 58 MoleculeACE and Polaris tasks show that MolPAIR improves performance on 46 tasks across multiple molecular representations and TFM backbones, demonstrating that explicit molecular comparisons strengthen tabular in‑context learning for structural generalization.
arXiv:2511.20510v3 Announce Type: replace Abstract: Molecule generation from extremely limited training data is a key challenge in drug discovery. Existing fragment-based methods are more suitable th...
TopU-LBVS is a new multi‑target benchmark for ligand‑based virtual screening that addresses shortcomings of existing datasets by using hard‑negative decoys and a fixed 1:40 active‑to‑decoy ratio. It covers 93 protein targets across seven classes, provides three evaluation protocols (full, low‑data, and mini), and includes curated ChEMBL‑35 bioactivity data with property‑matched, structurally similar decoys. The benchmark demonstrates that performance drops sharply when moving from random‑decoy to hard‑negative evaluation, and it releases data, splits, code, and baseline implementations for reproducible comparison.
The study investigates how different distribution shifts affect the evaluation of drug‑target affinity (DTA) models, using 718,800 drug‑protein pairs from ChEMBL and BindingDB. It compares a baseline Morgan‑fingerprint + protein‑CNN model with 12 architectures that combine four drug representations and three ESM‑2 interaction modes, finding that mean validation RMSE rises significantly under protein‑cluster and dual out‑of‑distribution (OOD) scenarios. Model rankings remain consistent across chemical shifts but diverge under protein and dual OOD, indicating that architecture selection depends on the specific extrapolation context rather than just average error or training‑set size. Why it matters: The results suggest that DTA benchmarks should be designed to reflect the chemical and target shifts expected in real deployment, ensuring that chosen models perform reliably when applied to new chemical series or protein targets.
TopU-LBVS is a new multi‑target benchmark for ligand‑based virtual screening that addresses shortcomings of previous datasets by using hard‑negative decoys and a fixed 1:40 active‑to‑decoy ratio. It covers 93 protein targets across seven classes, provides three evaluation protocols (full, low‑data, and mini), and includes curated ChEMBL‑35 bioactivity data with property‑matched, structurally similar decoys to reduce shortcut learning. The benchmark comes with released data, fixed splits, evaluation code, and baseline implementations for reproducible comparison of LBVS and molecular representation methods.
arXiv:2607. 28437v1 Announce Type: new Abstract: Molecular optimization is commonly performed under a limited oracle budget, which makes deciding what to evaluate as important as deciding what to generate.
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.
R-GroundBench is a new diagnostic benchmark for evaluating AI models on R‑group grounding in Markush molecular editing, derived from real pharmaceutical patents. It includes a Multiple‑Choice VQA track with varying difficulty and modality splits, as well as an open‑ended Generation track. Experiments show a large performance gap: models score over 90% on easy VQA but drop to 56–66% on hard VQA, and generation exact match stays below 20% (and under 8% with visual input).