LLMs with improved chemical reasoning capabilities in the other two sub-tasks.

Spectroscopic techniques are essential tools for determining the structure of molecules.

Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym - the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data.

Neural Information Processing Systems http://nips.cc/

Spectroscopic techniques are essential tools for determining the structure of molecules. Different spectroscopic techniques, such as Nuclear magnetic resonance (NMR), Infrared spectroscopy, and Mass Spectrometry, provide insight into the molecular structure, including the presence or absence of functional groups.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality MS/MS spectra and defines three MS/MS annotation challenges: \textit{de novo} molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community.

With the widespread application of multimodal large language models in scientific intelligence, there is an urgent need for more challenging evaluation benchmarks to assess their ability to understand complex scientific data. Scientific tables, as core carriers of knowledge representation, combine text, symbols, and graphics, forming a typical multimodal reasoning scenario. However, existing benchmarks are mostly focused on general domains, failing to reflect the unique structural complexity and domain-specific semantics inherent in scientific research. Chemical tables are particularly representative: they intertwine structured variables such as reagents, conditions, and yields with visual symbols like molecular structures and chemical formulas, posing significant challenges to models in cross-modal alignment and semantic parsing. To address this, we propose ChemTable-a large scale benchmark of chemical tables constructed from real-world literature, containing expert-annotated cell layouts, logical structures, and domain-specific labels. It supports two core tasks: (1) table recognition (structure and content extraction); and (2) table understanding (descriptive and reasoning-based question answering). Evaluation on ChemTable shows that while mainstream multimodal models perform reasonably well in layout parsing, they still face significant limitations when handling critical elements such as molecular structures and symbolic conventions. Closed-source models lead overall but still fall short of human-level performance. This work provides a realistic testing platform for evaluating scientific multimodal understanding, revealing the current bottlenecks in domain-specific reasoning and advancing the development of intelligent systems for scientific research.

Diffusion models show promise for 3D molecular generation, but face a fundamental trade-off between sampling efficiency and conformational accuracy. While flow-based models are fast, they often produce geometrically inaccurate structures, as they have difficulty capturing the multimodal distributions of molecular conformations. In contrast, denoising diffusion models are more accurate but suffer from slow sampling, a limitation attributed to sub-optimal integration between diffusion dynamics and SE(3)-equivariant architectures. To address this, we propose VEDA, a unified SE(3)-equivariant framework that combines variance-exploding diffusion with annealing to efficiently generate conformationally accurate 3D molecular structures. Specifically, our key technical contributions include: (1) a VE schedule that enables noise injection functionally analogous to simulated annealing, improving 3D accuracy and reducing relaxation energy; (2) a novel preconditioning scheme that reconciles the coordinate-predicting nature of SE(3)-equivariant networks with a residual-based diffusion objective, and (3) a new arcsin-based scheduler that concentrates sampling in critical intervals of the logarithmic signal-to-noise ratio. On the QM9 and GEOM-DRUGS datasets, VEDA matches the sampling efficiency of flow-based models, achieving state-of-the-art valency stability and validity with only 100 sampling steps. More importantly, VEDA's generated structures are remarkably stable, as measured by their relaxation energy during GFN2-xTB optimization. The median energy change is only 1.72 kcal/mol, significantly lower than the 32.3 kcal/mol from its architectural baseline, SemlaFlow. Our framework demonstrates that principled integration of VE diffusion with SE(3)-equivariant architectures can achieve both high chemical accuracy and computational efficiency.