SpectraLLM: Uncovering the Ability of LLMs for Molecule Structure Elucidation from Multi-Spectra

YUNYUE SU, Jiahui Chen, Zao Jiang, Zhenyi Zhong, Liang Wang, Qiang Liu, Zhaoxiang Zhang

International Conference on Learning Representations 2026 (ICLR 2026) Conference

Automated molecular structure elucidation remains challenging, as existing approaches often depend on pre-compiled databases or restrict themselves to single spectroscopic modalities. Here we introduce SpectraLLM, a large language model that performs end-to-end structure prediction by reasoning over one or multiple spectra. Unlike conventional spectrum-to-structure pipelines, SpectraLLM represents both continuous (IR, Raman, UV-Vis, NMR) and discrete (MS) modalities in a shared language space, enabling it to capture substructural patterns that are complementary across different spectral types. We pretrain and fine-tune the model on small-molecule domains and evaluate it on four public benchmark datasets. SpectraLLM achieves state-of-the-art performance, substantially surpassing single-modality baselines. Moreover, it demonstrates strong robustness in unimodal settings and further improves prediction accuracy when jointly reasoning over diverse spectra, establishing a scalable paradigm for language-based spectroscopic analysis.